Karplus, Martin

Publication with MATCHING institution:

Dobson CM, Šali A, Karplus M (1998) Protein Folding: A Perspective from Theory and Experiment. Angewandte Chemie -
International Edition. [IF=2.456, Cited=150, 29711488].
Karplus M, Prévost M, Tidor B, Wodak S (1991) Simulation analysis of the stability mutants R96H of bacteriophage T4
lysozyme and I96A of barnase. None. [IF=None, Cited=0, 1814697].
Karplus M (2014) Development of multiscale models for complex chemical systems: from H+H₂ to biomolecules (Nobel
Lecture). Angewandte Chemie - International Edition. [IF=2.456, Cited=29, 25066036].
Karplus M (2003) Molecular dynamics of biological macromolecules: a brief history and perspective. Biopolymers.
[IF=0.522, Cited=32, 12601794].
Conti S, Ovchinnikov V, Karplus M (2022) ppdx: Automated modeling of protein-protein interaction descriptors for use
with machine learning. Journal of Computational Chemistry. [IF=1.045, Cited=1, 35930347].
Bruccoleri RE, Karplus M (1986) Spatially constrained minimization of macromolecules. Journal of Computational
Chemistry. [IF=1.045, Cited=10, 29160574].
Karplus M (2010) Dynamical aspects of molecular recognition. Journal of Molecular Recognition. [IF=0.58, Cited=9, 20151415].
Buchko GW, Pulavarti SVSRK, Ovchinnikov V, ..., Bahl CD (2018) Cytosolic expression, solution structures, and molecular
dynamics simulation of genetically encodable disulfide-rich de novo designed peptides. Protein Science. [IF=1.97,
Cited=8, 30152054].
Karplus M, Weaver DL (1994) Protein folding dynamics: the diffusion-collision model and experimental data. Protein
Science. [IF=1.97, Cited=220, 8003983].
Karplus M, Ichiye T (1996) Comment on a "fluctuation and cross correlation analysis of protein motions observed in
nanosecond molecular dynamics simulations". Journal of Molecular Biology. [IF=1.281, Cited=35, 8913294].
Ovchinnikov V, Munasinghe A, Karplus M (2022) Molecular Simulation of Stapled Peptides. Methods in Molecular Biology.
[IF=0.413, Cited=0, 35298819].
Conti S, Karplus M (2023) A Computational Framework for Determining the Breadth of Antibodies Against Highly Mutable
Pathogens. Methods in Molecular Biology. [IF=0.413, Cited=0, 36346605].
Karplus M (1988) Proteins: dynamics and function. None. [IF=None, Cited=0, 3066337].
Karplus M, Post CB (1996) Simulations of lysozyme: internal motions and the reaction mechanism. None. [IF=None,
Cited=1, 8765298].
Karplus M, Ichiye T, Pettitt BM (1987) Configurational entropy of native proteins. Biophysical Journal. [IF=0.842,
Cited=103, 3427197].
Meuwly M, Karplus M (2021) The functional role of the hemoglobin-water interface. Molecular Aspects of Medicine.
[IF=2.862, Cited=0, 34756740].
Karplus M, Gao YQ (2004) Biomolecular motors: the F1-ATPase paradigm. Current Opinion in Structural Biology. [IF=1.4,
Cited=33, 15093841].
Ovchinnikov V, Conti S, Lau EY, ..., Karplus M (2020) Microsecond Molecular Dynamics Simulations of Proteins Using a
Quasi-Equilibrium Solvation Shell Model. Journal of Chemical Theory and Computation. [IF=1.512, Cited=3, 32045240].
Pezzella M, El Hage K, Niesen MJM, ..., Karplus M (2020) Water Dynamics Around Proteins: T- and R-States of Hemoglobin
and Melittin. Journal of Physical Chemistry B. [IF=0.893, Cited=7, 32589026].
Ovchinnikov V, Karplus M (2023) Free Energy Simulations of Receptor-Binding Domain Opening of the SARS-CoV-2 Spike
Indicate a Barrierless Transition with Slow Conformational Motions. Journal of Physical Chemistry B. [IF=0.893,
Cited=1, 37756691].
Ovchinnikov V, Nam K, Karplus M (2016) A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates
from Restrained Molecular Simulations of Diffusive Processes. Journal of Physical Chemistry B. [IF=0.893, Cited=8, 27135391].
Simonson T, Archontis G, Karplus M (2002) Free energy simulations come of age: protein-ligand recognition. Accounts of
Chemical Research. [IF=3.533, Cited=170, 12069628].
Ma A, Hu J, Karplus M (2006) Implications of alternative substrate binding modes for catalysis by uracil-DNA
glycosylase: an apparent discrepancy resolved. Biochemistry. [IF=0.753, Cited=5, 17105188].
Zheng G, Schaefer M, Karplus M (2013) Hemoglobin Bohr effects: atomic origin of the histidine residue contributions.
Biochemistry. [IF=0.753, Cited=13, 24224786].
Wu Y, Gao YQ, Karplus M (2007) A kinetic model of coordinated myosin V. Biochemistry. [IF=0.753, Cited=11, 17487986].
So SS, van Helden SP, van Geerestein VJ, Karplus M (2000) Quantitative structure-activity relationship studies of
progesterone receptor binding steroids. None. [IF=None, Cited=7, 10850780].
Cui Q, Karplus M (2001) Triosephosphate isomerase: a theoretical comparison of alternative pathways. Journal of the
American Chemical Society. [IF=2.573, Cited=38, 11456876].
Joseph-McCarthy D, Tsang SK, Filman DJ, ..., Karplus M (2001) Use of MCSS to design small targeted libraries:
application to picornavirus ligands. Journal of the American Chemical Society. [IF=2.573, Cited=14, 11749532].
Lopez X, Dejaegere A, Karplus M (2001) Solvent effects on the reaction coordinate of the hydrolysis of phosphates and
sulfates: application of Hammond and anti-Hammond postulates to understand hydrolysis in solution. Journal of the
American Chemical Society. [IF=2.573, Cited=12, 11716732].
Lopez X, Schaefer M, Dejaegere A, Karplus M (2002) Theoretical evaluation of pK(a) in phosphoranes: implications for
phosphate ester hydrolysis. Journal of the American Chemical Society. [IF=2.573, Cited=41, 11982365].
Cui Q, Karplus M (2002) Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions:
effect of geometry and tunneling on proton-transfer rate constants. Journal of the American Chemical Society. [IF=2.573,
Cited=55, 11902900].
Michielin O, Zoete V, Gierasch TM, ..., Karplus M (2002) Conformational analysis of a stereochemically complete set of
cis-enediol peptide analogues. Journal of the American Chemical Society. [IF=2.573, Cited=4, 12224961].
Vendruscolo M, Paci E, Dobson CM, Karplus M (2003) Rare fluctuations of native proteins sampled by equilibrium hydrogen
exchange. Journal of the American Chemical Society. [IF=2.573, Cited=72, 14677926].
Moulin E, Zoete V, Barluenga S, ..., Winssinger N (2005) Design, synthesis, and biological evaluation of HSP90
inhibitors based on conformational analysis of radicicol and its analogues. Journal of the American Chemical Society.
[IF=2.573, Cited=55, 15884943].
Best RB, Clarke J, Karplus M (2004) The origin of protein sidechain order parameter distributions. Journal of the
American Chemical Society. [IF=2.573, Cited=33, 15212494].
Nam K, Verdine GL, Karplus M (2009) Analysis of an anomalous mutant of MutM DNA glycosylase leads to new insights into
the catalytic mechanism. Journal of the American Chemical Society. [IF=2.573, Cited=12, 19961158].
So SS, Karplus M (1996) Evolutionary optimization in quantitative structure-activity relationship: an application of
genetic neural networks. Journal of Medicinal Chemistry. [IF=1.655, Cited=99, 8691483].
So SS, Karplus M (1996) Genetic neural networks for quantitative structure-activity relationships: improvements and
application of benzodiazepine affinity for benzodiazepine/GABAA receptors. Journal of Medicinal Chemistry. [IF=1.655,
Cited=44, 8978853].
So SS, Karplus M (1997) Three-dimensional quantitative structure-activity relationships from molecular similarity
matrices and genetic neural networks. 1. Method and validations. Journal of Medicinal Chemistry. [IF=1.655, Cited=52, 9435904].
So SS, Karplus M (1997) Three-dimensional quantitative structure-activity relationships from molecular similarity
matrices and genetic neural networks. 2. Applications. Journal of Medicinal Chemistry. [IF=1.655, Cited=28, 9435905].
Chekmarev SF, Krivov SV, Karplus M (2005) Folding time distributions as an approach to protein folding kinetics. Journal
of Physical Chemistry B. [IF=0.893, Cited=13, 16863198].
Nutt DR, Karplus M, Meuwly M (2005) Potential energy surface and molecular dynamics of MbNO: existence of an unsuspected
FeON minimum. Journal of Physical Chemistry B. [IF=0.893, Cited=9, 16853735].
Leclerc F, Karplus M (2006) Two-metal-ion mechanism for hammerhead-ribozyme catalysis. Journal of Physical Chemistry B.
[IF=0.893, Cited=18, 16494354].
Chekmarev SF, Krivov SV, Karplus M (2006) Folding of ubiquitin: a simple model describes the strange kinetics. Journal
of Physical Chemistry B. [IF=0.893, Cited=6, 16640446].
Luo G, Andricioaei I, Xie XS, ..., Karplus M (2006) Dynamic distance disorder in proteins is caused by trapping. Journal
of Physical Chemistry B. [IF=0.893, Cited=39, 16686476].
Krivov SV, Karplus M (2006) One-dimensional free-energy profiles of complex systems: progress variables that preserve
the barriers. Journal of Physical Chemistry B. [IF=0.893, Cited=47, 16800603].
Golosov AA, Karplus M (2007) Probing polar solvation dynamics in proteins: a molecular dynamics simulation analysis.
Journal of Physical Chemistry B. [IF=0.893, Cited=39, 17249715].
Palyanov AY, Krivov SV, Karplus M, Chekmarev SF (2007) A lattice protein with an amyloidogenic latent state: stability
and folding kinetics. Journal of Physical Chemistry B. [IF=0.893, Cited=7, 17315918].
Maragakis P, Spichty M, Karplus M (2008) A differential fluctuation theorem. Journal of Physical Chemistry B. [IF=0.893,
Cited=10, 18331019].
Luo G, Karplus M (2011) Determining the conformational change that accompanies donor-acceptor distance fluctuations: an
umbrella sampling analysis. Journal of Physical Chemistry B. [IF=0.893, Cited=1, 21619043].
Ovchinnikov V, Karplus M (2012) Analysis and elimination of a bias in targeted molecular dynamics simulations of
conformational transitions: application to calmodulin. Journal of Physical Chemistry B. [IF=0.893, Cited=38, 22409258].
Ovchinnikov V, Cecchini M, Karplus M (2013) A simplified confinement method for calculating absolute free energies and
free energy and entropy differences. Journal of Physical Chemistry B. [IF=0.893, Cited=12, 23268557].
Kalgin IV, Caflisch A, Chekmarev SF, Karplus M (2013) New insights into the folding of a β-sheet miniprotein in a
reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. Journal
of Physical Chemistry B. [IF=0.893, Cited=18, 23621790].
Kalgin IV, Chekmarev SF, Karplus M (2014) First passage analysis of the folding of a β-sheet miniprotein: is it more
realistic than the standard equilibrium approach? Journal of Physical Chemistry B. [IF=0.893, Cited=6, 24669953].
Krivov SV, Muff S, Caflisch A, Karplus M (2008) One-dimensional barrier-preserving free-energy projections of a beta-
sheet miniprotein: new insights into the folding process. Journal of Physical Chemistry B. [IF=0.893, Cited=37, 18590307].
Maragakis P, van der Vaart A, Karplus M (2009) Gaussian-mixture umbrella sampling. Journal of Physical Chemistry B.
[IF=0.893, Cited=20, 19284746].
Cecchini M, Krivov SV, Spichty M, Karplus M (2009) Calculation of free-energy differences by confinement simulations.
Application to peptide conformers. Journal of Physical Chemistry B. [IF=0.893, Cited=28, 19552392].
Kalgin IV, Karplus M, Chekmarev SF (2009) Folding of a SH3 domain: standard and "hydrodynamic" analyses. Journal of
Physical Chemistry B. [IF=0.893, Cited=12, 19711956].
MacKerell AD, Bashford D, Bellott M, ..., Karplus M (1998) All-atom empirical potential for molecular modeling and
dynamics studies of proteins. Journal of Physical Chemistry B. [IF=0.893, Cited=1000, 24889800].
Karplus M, Petsko GA (1990) Molecular dynamics simulations in biology. Nature. [IF=11.591, Cited=357, 2215695].
Karplus M (2011) Behind the folding funnel diagram. Nature Chemical Biology. [IF=2.623, Cited=56, 21685880].
Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. None. [IF=None, Cited=1000, 12198485].
Shigdel UK, Ovchinnikov V, Lee SJ, ..., Verdine GL (2020) The trajectory of intrahelical lesion recognition and
extrusion by the human 8-oxoguanine DNA glycosylase. Nature Communications. [IF=3.268, Cited=12, 32895378].
Karplus M, Evanseck JD, Joseph D, ..., Field MJ (1992) Simulation analysis of triose phosphate isomerase: conformational
transition and catalysis. None. [IF=None, Cited=5, 1290934].
Mulholland AJ, Karplus M (1996) Simulations of enzymic reactions. Biochemical Society Transactions. [IF=0.925, Cited=5, 8674677].
Yang W, Bitetti-Putzer R, Karplus M (2004) Free energy simulations: use of reverse cumulative averaging to determine the
equilibrated region and the time required for convergence. Journal of Chemical Physics. [IF=1.184, Cited=55, 15268405].
Yang W, Bitetti-Putzer R, Karplus M (2004) Chaperoned alchemical free energy simulations: a general method for QM, MM,
and QM/MM potentials. Journal of Chemical Physics. [IF=1.184, Cited=18, 15267955].
Wan S, Stote RH, Karplus M (2004) Calculation of the aqueous solvation energy and entropy, as well as free energy, of
simple polar solutes. Journal of Chemical Physics. [IF=1.184, Cited=30, 15538876].
van der Vaart A, Karplus M (2005) Simulation of conformational transitions by the restricted perturbation-targeted
molecular dynamics method. Journal of Chemical Physics. [IF=1.184, Cited=43, 15836253].
Bitetti-Putzer R, Yang W, Karplus M (2006) Conformational sampling via a self-regulating effective energy surface.
Journal of Chemical Physics. [IF=1.184, Cited=12, 16689598].
van der Vaart A, Karplus M (2007) Minimum free energy pathways and free energy profiles for conformational transitions
based on atomistic molecular dynamics simulations. Journal of Chemical Physics. [IF=1.184, Cited=26, 17477588].
Maragakis P, Ritort F, Bustamante C, ..., Crooks GE (2008) Bayesian estimates of free energies from nonequilibrium work
data in the presence of instrument noise. Journal of Chemical Physics. [IF=1.184, Cited=25, 18624511].
Ovchinnikov V, Karplus M, Vanden-Eijnden E (2011) Free energy of conformational transition paths in biomolecules: the
string method and its application to myosin VI. Journal of Chemical Physics. [IF=1.184, Cited=70, 21361558].
Zheng G, Niklasson AMN, Karplus M (2011) Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics
using the density-functional tight-binding method. Journal of Chemical Physics. [IF=1.184, Cited=20, 21806105].
Ovchinnikov V, Karplus M (2014) Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-
temperature string method. Journal of Chemical Physics. [IF=1.184, Cited=10, 24811667].
Ovchinnikov V, Conti S, Karplus M (2020) A restrained locally enhanced sampling method (RLES) for finding free energy
minima in complex systems. Journal of Chemical Physics. [IF=1.184, Cited=0, 33003727].
Salehi SM, Pezzella M, Willard A, ..., Karplus M (2023) Water dynamics around T₀ vs R₄ of
hemoglobin from local hydrophobicity analysis. Journal of Chemical Physics. [IF=1.184, Cited=0, 36641390].
Yang W, Gao YQ, Cui Q, ..., Karplus M (2003) The missing link between thermodynamics and structure in F1-ATPase.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=64, 12552084].
Hwang W, Zhang S, Kamm RD, Karplus M (2004) Kinetic control of dimer structure formation in amyloid fibrillogenesis.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=98, 15326301].
Krivov SV, Karplus M (2004) Hidden complexity of free energy surfaces for peptide (protein) folding. Proceedings of the
National Academy of Sciences of the United States of America. [IF=2.765, Cited=165, 15466711].
Karplus M, Kuriyan J (2005) Molecular dynamics and protein function. Proceedings of the National Academy of Sciences of
the United States of America. [IF=2.765, Cited=474, 15870208].
Taly A, Corringer PJ, Grutter T, ..., Changeux JP (2006) Implications of the quaternary twist allosteric model for the
physiology and pathology of nicotinic acetylcholine receptors. Proceedings of the National Academy of Sciences of the
United States of America. [IF=2.765, Cited=73, 17077146].
Pu J, Karplus M (2008) How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase. Proceedings of the
National Academy of Sciences of the United States of America. [IF=2.765, Cited=64, 18216260].
Krivov SV, Karplus M (2008) Diffusive reaction dynamics on invariant free energy profiles. Proceedings of the National
Academy of Sciences of the United States of America. [IF=2.765, Cited=50, 18772379].
Khalil AS, Appleyard DC, Labno AK, ..., Lang MJ (2008) Kinesin's cover-neck bundle folds forward to generate force.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=81, 19047639].
Grinthal A, Adamovic I, Weiner B, ..., Kleckner N (2010) PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an
elastic connector that links force and catalysis. Proceedings of the National Academy of Sciences of the United States
of America. [IF=2.765, Cited=74, 20133745].
Rao F, Karplus M (2010) Protein dynamics investigated by inherent structure analysis. Proceedings of the National
Academy of Sciences of the United States of America. [IF=2.765, Cited=29, 20435910].
Paci E, Karplus M (2000) Unfolding proteins by external forces and temperature: the importance of topology and
energetics. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=180, 10823892].
Karplus M (2010) Role of conformation transitions in adenylate kinase. Proceedings of the National Academy of Sciences
of the United States of America. [IF=2.765, Cited=16, 20424124].
Fischer S, Olsen KW, Nam K, Karplus M (2011) Unsuspected pathway of the allosteric transition in hemoglobin. Proceedings
of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=46, 21415366].
Calimet N, Simoes M, Changeux JP, ..., Cecchini M (2013) A gating mechanism of pentameric ligand-gated ion channels.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=80, 24043807].
Gao YQ, Yang W, Marcus RA, Karplus M (2003) A model for the cooperative free energy transduction and kinetics of ATP
hydrolysis by F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765,
Cited=34, 14500780].
Guo H, Cui Q, Lipscomb WN, Karplus M (2001) Substrate conformational transitions in the active site of chorismate
mutase: their role in the catalytic mechanism. Proceedings of the National Academy of Sciences of the United States of
America. [IF=2.765, Cited=32, 11481470].
Nam K, Pu J, Karplus M (2014) Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase
mechanism. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=27, 25453082].
Ovchinnikov V, Stone TA, Deber CM, Karplus M (2018) Structure of the EmrE multidrug transporter and its use for
inhibitor peptide design. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765,
Cited=24, 30082384].
Hwang W, Karplus M (2019) Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=38, 31506355].
Nam K, Karplus M (2019) Insights into the origin of the high energy-conversion efficiency of F₁-ATPase.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=9, 31341091].
Conti S, Kaczorowski KJ, Song G, ..., Karplus M (2021) Design of immunogens to elicit broadly neutralizing antibodies
against HIV targeting the CD4 binding site. Proceedings of the National Academy of Sciences of the United States of
America. [IF=2.765, Cited=4, 33637649].
Vendruscolo M, Paci E, Karplus M, Dobson CM (2003) Structures and relative free energies of partially folded states of
proteins. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=35, 14657374].
Paci E, Clarke J, Steward A, ..., Karplus M (2003) Self-consistent determination of the transition state for protein
folding: application to a fibronectin type III domain. Proceedings of the National Academy of Sciences of the United
States of America. [IF=2.765, Cited=37, 12515856].
Honig B, Hudson B, Sykes BD, Karplus M (1971) Ring orientation in -ionone and retinals. Proceedings of the National
Academy of Sciences of the United States of America. [IF=2.765, Cited=21, 5288377].
Karplus S, Karplus M (1972) Nuclear magnetic resonance determination of the angle psi in peptides. Proceedings of the
National Academy of Sciences of the United States of America. [IF=2.765, Cited=7, 4508315].
Levy RM, Perahia D, Karplus M (1982) Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and
deviation from harmonic behavior. Proceedings of the National Academy of Sciences of the United States of America.
[IF=2.765, Cited=65, 16593164].
Holley LH, Karplus M (1989) Protein secondary structure prediction with a neural network. Proceedings of the National
Academy of Sciences of the United States of America. [IF=2.765, Cited=141, 2911565].
Kuczera K, Gao J, Tidor B, Karplus M (1990) Free energy of sickling: A simulation analysis. Proceedings of the National
Academy of Sciences of the United States of America. [IF=2.765, Cited=12, 2236057].
Smith J, Kuczera K, Karplus M (1990) Dynamics of myoglobin: comparison of simulation results with neutron scattering
spectra. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=73, 2304919].
Holley LH, Goudsmit J, Karplus M (1991) Prediction of optimal peptide mixtures to induce broadly neutralizing antibodies
to human immunodeficiency virus type 1. Proceedings of the National Academy of Sciences of the United States of America.
[IF=2.765, Cited=11, 1862103].
Kuczera K, Lambry JC, Martin JL, Karplus M (1993) Nonexponential relaxation after ligand dissociation from myoglobin: a
molecular dynamics simulation. Proceedings of the National Academy of Sciences of the United States of America.
[IF=2.765, Cited=26, 8516332].
Caflisch A, Karplus M (1994) Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores
and secondary structure of barnase. Proceedings of the National Academy of Sciences of the United States of America.
[IF=2.765, Cited=84, 8127876].
Dinner AR, Sali A, Karplus M (1996) The folding mechanism of larger model proteins: role of native structure.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=42, 8710875].
Ma J, Karplus M (1997) Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=98, 9342335].
Zhou Y, Karplus M (1997) Folding thermodynamics of a model three-helix-bundle protein. Proceedings of the National
Academy of Sciences of the United States of America. [IF=2.765, Cited=99, 9405629].
Ma J, Karplus M (1998) The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proceedings of the National
Academy of Sciences of the United States of America. [IF=2.765, Cited=115, 9671707].
Ma J, Zheng X, Schnappauf G, ..., Lipscomb WN (1998) Yeast chorismate mutase in the R state: simulations of the active
site. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=7, 9843942].
Dinner AR, Lazaridis T, Karplus M (1999) Understanding beta-hairpin formation. Proceedings of the National Academy of
Sciences of the United States of America. [IF=2.765, Cited=182, 10430896].
Karplus M, Gao YQ, Ma J, ..., Yang W (2005) Protein structural transitions and their functional role. Philosophical
transactions. Series A, Mathematical, physical, and engineering sciences. [IF=1.42, Cited=18, 15664887].
Karplus M, Brünger AT, Elber R, Kuriyan J (1987) Molecular dynamics: applications to proteins. Cold Spring Harbor
Symposia on Quantitative Biology. [IF=0.889, Cited=8, 3454267].
Meroz Y, Ovchinnikov V, Karplus M (2017) Coexisting origins of subdiffusion in internal dynamics of proteins. Physical
Review E. [IF=0.912, Cited=6, 28709262].
Fallah-Araghi A, Meguellati K, Baret JC, ..., Griffiths AD (2014) Enhanced chemical synthesis at soft interfaces: a
universal reaction-adsorption mechanism in microcompartments. Physical Review Letters. [IF=2.288, Cited=85, 24484045].
Garcia-Viloca M, Gao J, Karplus M, Truhlar DG (2004) How enzymes work: analysis by modern rate theory and computer
simulations. Science. [IF=7.729, Cited=422, 14716003].
Michnick SW, Rosen MK, Wandless TJ, ..., Schreiber SL (1991) Solution structure of FKBP, a rotamase enzyme and receptor
for FK506 and rapamycin. Science. [IF=7.729, Cited=149, 1709301].
Brünger AT, Kuriyan J, Karplus M (1987) Crystallographic R factor refinement by molecular dynamics. Science. [IF=7.729,
Cited=1000, 17810339].
Brünger AT, Campbell RL, Clore GM, ..., Teeter MM (1987) Solution of a protein crystal structure with a model obtained
from NMR interproton distance restraints. Science. [IF=7.729, Cited=20, 17782253].
Joseph D, Petsko GA, Karplus M (1990) Anatomy of a conformational change: hinged "lid" motion of the triosephosphate
isomerase loop. Science. [IF=7.729, Cited=163, 2402636].
Gao J, Kuczera K, Tidor B, Karplus M (1989) Hidden thermodynamics of mutant proteins: a molecular dynamics analysis.
Science. [IF=7.729, Cited=115, 2727695].
Lazaridis T, Karplus M (1997) "New view" of protein folding reconciled with the old through multiple unfolding
simulations. Science. [IF=7.729, Cited=290, 9395391].
Elber R, Karplus M (1987) Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin.
Science. [IF=7.729, Cited=285, 3798113].
Irikura KK, Tidor B, Brooks BR, Karplus M (1985) Transition from B to Z DNA: contribution of internal fluctuations to
the configurational entropy difference. Science. [IF=7.729, Cited=30, 3839596].
Karplus M (2006) Spinach on the ceiling: a theoretical chemist's return to biology. None. [IF=None, Cited=9, 16689626].
Conti S, Karplus M (2019) Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine
learning. PLoS Computational Biology. [IF=1.278, Cited=6, 30970017].
Conti S, Ovchinnikov V, Faris JG, ..., Sprenger KG (2022) Multiscale affinity maturation simulations to elicit broadly
neutralizing antibodies against HIV. PLoS Computational Biology. [IF=1.278, Cited=4, 35442968].
Ovchinnikov V, Karplus M (2022) A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell
Receptor Avidity in Epitope Subdominance. Frontiers in Immunology. [IF=1.49, Cited=2, 35371013].
Sliz P, Michielin O, Cerottini JC, ..., Wiley DC (2001) Crystal structures of two closely related but antigenically
distinct HLA-A2/melanocyte-melanoma tumor-antigen peptide complexes. Journal of Immunology. [IF=0.939, Cited=60, 11544315].
Hwang W, Lang MJ, Karplus M (2017) Kinesin motility is driven by subdomain dynamics. eLife. [IF=1.743, Cited=21, 29111975].
Klein M, Krivov SV, Ferrer AJ, ..., Karplus M (2017) Exploratory search during directed navigation in C. elegans
and Drosophila larva. eLife. [IF=1.743, Cited=17, 29083306].
Ovchinnikov V, Louveau JE, Barton JP, ..., Chakraborty AK (2018) Role of framework mutations and antibody flexibility in
the evolution of broadly neutralizing antibodies. eLife. [IF=1.743, Cited=43, 29442996].
El Hage K, Hédin F, Gupta PK, ..., Karplus M (2018) Valid molecular dynamics simulations of human hemoglobin require a
surprisingly large box size. eLife. [IF=1.743, Cited=35, 29998846].
El Hage K, Hédin F, Gupta PK, ..., Karplus M (2019) Response to comment on 'Valid molecular dynamics simulations of
human hemoglobin require a surprisingly large box size'. eLife. [IF=1.743, Cited=9, 31219783].

Publication with MISSING institution:

Landau D, Mordechai J, Karplus M, Carmi R (1997) Inheritance of familial congenital isolated anorectal malformations:
case report and review. None. [IF=None, Cited=15, 9268096].
Joseph-McCarthy D, Hogle JM, Karplus M (1997) Use of the multiple copy simultaneous search (MCSS) method to design a new
class of picornavirus capsid binding drugs. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=19, 9294865].
van Vlijmen HW, Schaefer M, Karplus M (1998) Improving the accuracy of protein pKa calculations: conformational
averaging versus the average structure. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=86, 9779784].
Dinner AR, So SS, Karplus M (1998) Use of quantitative structure-property relationships to predict the folding ability
of model proteins. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=13, 9779787].
Dinner AR, Abkevich V, Shakhnovich E, Karplus M (1999) Factors that affect the folding ability of proteins. Proteins:
Structure, Function and Bioinformatics. [IF=0.897, Cited=25, 10090284].
Lazaridis T, Karplus M (1999) Effective energy function for proteins in solution. Proteins: Structure, Function and
Bioinformatics. [IF=0.897, Cited=702, 10223287].
Dinner AR, Karplus M (2001) Comment on the Communication "The Key to Solving the Protein-Folding Problem Lies in an
Accurate Description of the Denatured State" by van Gunsteren et al. We thank Eugene Shakhnovich (Harvard University)
for pointing out the references on lattice polymer simulations and very helpful discussions. We also thank Wilfred van
Gunsteren for comments on the manuscript. A.R.D. is a Burroughs Wellcome Fund Hitchings-Elion Postdoctoral Fellow. The
work done at Harvard was supported in part by the National Institutes of Health. Angewandte Chemie - International
Edition. [IF=2.456, Cited=5, 12404364].
Abeliovich D, Carmi R, Karplus M, ..., Cohen MM (1979) Monosomy 21: a possible stepwise evolution of the karyotype.
None. [IF=None, Cited=15, 574719].
Carmi R, Abeliovich D, Bar-Ziv J, ..., Cohen MM (1980) Malformation syndrome associated with small extra chromosome.
None. [IF=None, Cited=7, 7395896].
Carmi R, Sofer S, Karplus M, ..., Bar-Ziv J (1982) Aplasia cutis congenita in two sibs discordant for pyloric atresia.
None. [IF=None, Cited=47, 6177243].
Abeliovich D, Katz M, Karplus M, Carmi R (1985) A de novo translocation, 14q21q, with a microchromosome-14p21p. None.
[IF=None, Cited=5, 2931981].
Guo H, Cui Q, Lipscomb WN, Karplus M (2003) Understanding the role of active-site residues in chorismate mutase
catalysis from molecular-dynamics simulations. Angewandte Chemie - International Edition. [IF=2.456, Cited=8, 12698486].
Brooks CL, Brünger A, Karplus M (1985) Active site dynamics in protein molecules: a stochastic boundary molecular-
dynamics approach. Biopolymers. [IF=0.522, Cited=131, 2410050].
Bruccoleri RE, Karplus M, McCammon JA (1986) The hinge-bending mode of a lysozyme-inhibitor complex. Biopolymers.
[IF=0.522, Cited=23, 3768485].
Ichiye T, Olafson BD, Swaminathan S, Karplus M (1986) Structure and internal mobility of proteins: a molecular dynamics
study of hen egg white lysozyme. Biopolymers. [IF=0.522, Cited=11, 3779015].
Bruccoleri RE, Karplus M (1987) Prediction of the folding of short polypeptide segments by uniform conformational
sampling. Biopolymers. [IF=0.522, Cited=220, 3801593].
Lee SY, Karplus M, Bashford D, Weaver D (1987) Brownian dynamics simulation of protein folding: a study of the
diffusion-collision model. Biopolymers. [IF=0.522, Cited=21, 3567323].
Bruccoleri RE, Karplus M (1990) Conformational sampling using high-temperature molecular dynamics. Biopolymers.
[IF=0.522, Cited=103, 2207289].
Karthikeyan G, Zambaldo C, Barluenga S, ..., Winssinger N (2012) Asymmetric synthesis of pochonin E and F, revision of
their proposed structure, and their conversion to potent Hsp90 inhibitors. Chemistry - A European Journal. [IF=0.899,
Cited=7, 22696415].
Clore GM, Nilges M, Sukumaran DK, ..., Gronenborn AM (1986) The three-dimensional structure of alpha1-purothionin in
solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO Journal.
[IF=2.114, Cited=127, 16453716].
Petrella RJ, Andricioaei I, Brooks BR, Karplus M (2003) An improved method for nonbonded list generation: rapid
determination of near-neighbor pairs. Journal of Computational Chemistry. [IF=1.045, Cited=13, 12497601].
Elstner M, Cui Q, Munih P, ..., Karplus M (2003) Modeling zinc in biomolecules with the self consistent charge-density
functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis. Journal of Computational
Chemistry. [IF=1.045, Cited=63, 12632471].
Schaefer M, Bartels C, Leclerc F, Karplus M (2001) Effective atom volumes for implicit solvent models: comparison
between Voronoi volumes and minimum fluctuation volumes. Journal of Computational Chemistry. [IF=1.045, Cited=38, 12116417].
Petrella RJ, Karplus M (2005) Electrostatic energies and forces computed without explicit interparticle interactions: a
linear time complexity formulation. Journal of Computational Chemistry. [IF=1.045, Cited=5, 15800892].
Brooks BR, Brooks CL, Mackerell AD, ..., Karplus M (2009) CHARMM: the biomolecular simulation program. Journal of
Computational Chemistry. [IF=1.045, Cited=1000, 19444816].
Korczyn AD, Sage JI, Karplus M (1978) Lack of limb motor asymmetry in the neonate. None. [IF=None, Cited=6, 739265].
Chandonia JM, Karplus M (1995) Neural networks for secondary structure and structural class predictions. Protein
Science. [IF=1.97, Cited=46, 7757016].
Chandonia JM, Karplus M (1996) The importance of larger data sets for protein secondary structure prediction with neural
networks. Protein Science. [IF=1.97, Cited=16, 8845767].
Lazaridis T, Lee I, Karplus M (1997) Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin.
Protein Science. [IF=1.97, Cited=65, 9416608].
Caves LS, Evanseck JD, Karplus M (1998) Locally accessible conformations of proteins: multiple molecular dynamics
simulations of crambin. Protein Science. [IF=1.97, Cited=255, 9541397].
Vitkup D, Ringe D, Karplus M, Petsko GA (2002) Why protein R-factors are so large: a self-consistent analysis. Proteins:
Structure, Function and Bioinformatics. [IF=0.897, Cited=23, 11835510].
Paci E, Vendruscolo M, Karplus M (2002) Native and non-native interactions along protein folding and unfolding pathways.
Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=42, 11948791].
Petrella RJ, Karplus M (2004) The role of carbon-donor hydrogen bonds in stabilizing tryptophan conformations. Proteins:
Structure, Function and Bioinformatics. [IF=0.897, Cited=10, 14997567].
Paci E, Friel CT, Lindorff-Larsen K, ..., Vendruscolo M (2004) Comparison of the transition state ensembles for folding
of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints. Proteins: Structure,
Function and Bioinformatics. [IF=0.897, Cited=30, 14747999].
Mattos C, Cohen JD, Green DF, ..., Karplus M (2004) X-ray structural and simulation analysis of a protein mutant: the
value of a combined approach. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=2, 15103635].
Zoete V, Meuwly M, Karplus M (2004) Investigation of glucose binding sites on insulin. Proteins: Structure, Function and
Bioinformatics. [IF=0.897, Cited=16, 15103621].
Zoete V, Meuwly M, Karplus M (2005) Study of the insulin dimerization: binding free energy calculations and per-residue
free energy decomposition. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=105, 16080143].
Archontis G, Watson KA, Xie Q, ..., Karplus M (2005) Glycogen phosphorylase inhibitors: a free energy perturbation
analysis of glucopyranose spirohydantoin analogues. Proteins: Structure, Function and Bioinformatics. [IF=0.897,
Cited=12, 16245298].
Kong Y, Karplus M (2009) Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis.
Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=76, 18618698].
Kuriyan J, Karplus M, Petsko GA (1987) Estimation of uncertainties in X-ray refinement results by use of perturbed
structures. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=18, 3447165].
Ichiye T, Karplus M (1987) Anisotropy and anharmonicity of atomic fluctuations in proteins: analysis of a molecular
dynamics simulation. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=38, 3447180].
Brünger AT, Karplus M (1988) Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction
comparison. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=281, 3227015].
Bashford D, Cohen FE, Karplus M, ..., Weaver DL (1988) Diffusion-collision model for the folding kinetics of myoglobin.
Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=31, 3237719].
Post CB, Dobson CM, Dobson CM, ..., Karplus M (1989) A molecular dynamics analysis of protein structural elements.
Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=25, 2798410].
Kuriyan J, Osapay K, Burley SK, ..., Karplus M (1991) Exploration of disorder in protein structures by X-ray restrained
molecular dynamics. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=58, 1946343].
Miranker A, Karplus M (1991) Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins:
Structure, Function and Bioinformatics. [IF=0.897, Cited=225, 1961699].
Ichiye T, Karplus M (1991) Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular
dynamics and normal mode simulations. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=446, 1749773].
Yapa K, Weaver DL, Karplus M (1992) Beta-sheet coil transitions in a simple polypeptide model. Proteins: Structure,
Function and Bioinformatics. [IF=0.897, Cited=10, 1557351].
Tidor B, Karplus M (1993) The contribution of cross-links to protein stability: a normal mode analysis of the
configurational entropy of the native state. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=40, 7680808].
Nakagawa S, Yu HA, Karplus M, Umeyama H (1993) Active site dynamics of acyl-chymotrypsin. Proteins: Structure, Function
and Bioinformatics. [IF=0.897, Cited=15, 8332606].
Eisen MB, Wiley DC, Karplus M, Hubbard RE (1994) HOOK: a program for finding novel molecular architectures that satisfy
the chemical and steric requirements of a macromolecule binding site. Proteins: Structure, Function and Bioinformatics.
[IF=0.897, Cited=81, 7937734].
Boresch S, Archontis G, Karplus M (1994) Free energy simulations: the meaning of the individual contributions from a
component analysis. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=44, 7824520].
Stote RH, Karplus M (1995) Zinc binding in proteins and solution: a simple but accurate nonbonded representation.
Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=149, 8539245].
Sali A, Potterton L, Yuan F, ..., Karplus M (1995) Evaluation of comparative protein modeling by MODELLER. Proteins:
Structure, Function and Bioinformatics. [IF=0.897, Cited=640, 8710825].
Miranker A, Karplus M (1995) An automated method for dynamic ligand design. Proteins: Structure, Function and
Bioinformatics. [IF=0.897, Cited=35, 8749844].
Dunbrack RL, Karplus M (1993) Backbone-dependent rotamer library for proteins. Application to side-chain prediction.
Journal of Molecular Biology. [IF=1.281, Cited=513, 8464064].
MacKerell AD, Sommer MS, Karplus M (1995) pH dependence of binding reactions from free energy simulations and
macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications
for catalysis. Journal of Molecular Biology. [IF=1.281, Cited=19, 7723031].
Sali A, Shakhnovich E, Karplus M (1994) Kinetics of protein folding. A lattice model study of the requirements for
folding to the native state. Journal of Molecular Biology. [IF=1.281, Cited=247, 8107095].
Tidor B, Karplus M (1994) The contribution of vibrational entropy to molecular association. The dimerization of insulin.
Journal of Molecular Biology. [IF=1.281, Cited=164, 8176732].
Mattos C, Petsko GA, Karplus M (1994) Analysis of two-residue turns in proteins. Journal of Molecular Biology.
[IF=1.281, Cited=34, 8182746].
Caflisch A, Karplus M (1995) Acid and thermal denaturation of barnase investigated by molecular dynamics simulations.
Journal of Molecular Biology. [IF=1.281, Cited=102, 7563082].
Boresch S, Karplus M (1995) The meaning of component analysis: decomposition of the free energy in terms of specific
interactions. Journal of Molecular Biology. [IF=1.281, Cited=65, 7500351].
van Vlijmen HW, Karplus M (1997) PDB-based protein loop prediction: parameters for selection and methods for
optimization. Journal of Molecular Biology. [IF=1.281, Cited=89, 9135125].
Ma J, Karplus M (1997) Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis.
Journal of Molecular Biology. [IF=1.281, Cited=74, 9398520].
van Vlijmen HW, Curry S, Schaefer M, Karplus M (1998) Titration calculations of foot-and-mouth disease virus capsids and
their stabilities as a function of pH. Journal of Molecular Biology. [IF=1.281, Cited=35, 9466910].
Archontis G, Simonson T, Moras D, Karplus M (1998) Specific amino acid recognition by aspartyl-tRNA synthetase studied
by free energy simulations. Journal of Molecular Biology. [IF=1.281, Cited=32, 9480772].
Martí-Renom MA, Stote RH, Querol E, ..., Karplus M (1998) Refolding of potato carboxypeptidase inhibitor by molecular
dynamics simulations with disulfide bond constraints. Journal of Molecular Biology. [IF=1.281, Cited=12, 9811548].
Schaefer M, Bartels C, Karplus M (1998) Solution conformations and thermodynamics of structured peptides: molecular
dynamics simulation with an implicit solvation model. Journal of Molecular Biology. [IF=1.281, Cited=120, 9826519].
Bartels C, Stote RH, Karplus M (1998) Characterization of flexible molecules in solution: the RGDW peptide. Journal of
Molecular Biology. [IF=1.281, Cited=10, 9878376].
Zhou Y, Vitkup D, Karplus M (1999) Native proteins are surface-molten solids: application of the Lindemann criterion for
the solid versus liquid state. Journal of Molecular Biology. [IF=1.281, Cited=78, 9917381].
Paci E, Karplus M (1999) Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics
simulations. Journal of Molecular Biology. [IF=1.281, Cited=189, 10329153].
Lazaridis T, Karplus M (1999) Discrimination of the native from misfolded protein models with an energy function
including implicit solvation. Journal of Molecular Biology. [IF=1.281, Cited=156, 10329155].
Blondel A, Renaud JP, Fischer S, ..., Karplus M (1999) Retinoic acid receptor: a simulation analysis of retinoic acid
binding and the resulting conformational changes. Journal of Molecular Biology. [IF=1.281, Cited=40, 10438609].
Zhou Y, Karplus M (1999) Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis. Journal of
Molecular Biology. [IF=1.281, Cited=53, 10543976].
Dinner AR, Karplus M (1999) Is protein unfolding the reverse of protein folding? A lattice simulation analysis. Journal
of Molecular Biology. [IF=1.281, Cited=52, 10493884].
Michielin O, Luescher I, Karplus M (2000) Modeling of the TCR-MHC-peptide complex. Journal of Molecular Biology.
[IF=1.281, Cited=19, 10903865].
Ma J, Sigler PB, Xu Z, Karplus M (2000) A dynamic model for the allosteric mechanism of GroEL. Journal of Molecular
Biology. [IF=1.281, Cited=140, 10970735].
Archontis G, Simonson T, Karplus M (2001) Binding free energies and free energy components from molecular dynamics and
Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. Journal of Molecular
Biology. [IF=1.281, Cited=51, 11237602].
Paci E, Smith LJ, Dobson CM, ..., Karplus M (2001) Exploration of partially unfolded states of human alpha-lactalbumin
by molecular dynamics simulation. Journal of Molecular Biology. [IF=1.281, Cited=34, 11237603].
Petrella RJ, Karplus M (2001) The energetics of off-rotamer protein side-chain conformations. Journal of Molecular
Biology. [IF=1.281, Cited=23, 11580256].
Paci E, Caflisch A, Plückthun A, Karplus M (2001) Forces and energetics of hapten-antibody dissociation: a biased
molecular dynamics simulation study. Journal of Molecular Biology. [IF=1.281, Cited=27, 11846569].
Zoete V, Michielin O, Karplus M (2002) Relation between sequence and structure of HIV-1 protease inhibitor complexes: a
model system for the analysis of protein flexibility. Journal of Molecular Biology. [IF=1.281, Cited=86, 11771964].
Grootenhuis PD, Karplus M (1996) Functionality map analysis of the active site cleft of human thrombin. Journal of
Computer-Aided Molecular Design. [IF=0.881, Cited=11, 8786410].
Fraser D, Weitzman S, Leiberman JR, ..., Karplus M (1994) Gestational diabetes among Bedouins in southern Israel:
comparison of prevalence and neonatal outcomes with the Jewish population. Acta Diabetologica. [IF=1.124, Cited=7, 7949226].
Gorodischer R, Karplus M (1982) Pharmacokinetic aspects of caffeine in premature infants with apnoea. European Journal
of Clinical Pharmacology. [IF=1.075, Cited=33, 7094974].
Evensen E, Joseph-McCarthy D, Weiss GA, ..., Karplus M (2007) Ligand design by a combinatorial approach based on
modeling and experiment: application to HLA-DR4. Journal of Computer-Aided Molecular Design. [IF=0.881, Cited=10, 17657565].
Wagman ME, Dobson CM, Dobson CM, ..., Karplus M (1980) Proton NMR studies of the association and folding of glucagon in
solution. FEBS Letters. [IF=0.871, Cited=15, 7428939].
Clore GM, Nilges M, Brünger AT, ..., Gronenborn AM (1987) A comparison of the restrained molecular dynamics and distance
geometry methods for determining three-dimensional structures of proteins on the basis of interproton distances. FEBS
Letters. [IF=0.871, Cited=20, 3030815].
Shulman RG, Glarum SH, Karplus M (1971) Electronic structure of cyanide complexes of hemes and heme proteins. Journal of
Molecular Biology. [IF=1.281, Cited=48, 5089700].
Szabo A, Karplus M (1972) A mathematical model for structure-function relations in hemoglobin. Journal of Molecular
Biology. [IF=1.281, Cited=116, 4648112].
Case DA, Karplus M (1978) Stereochemistry of carbon monoxide binding to myoglobin and hemoglobin. Journal of Molecular
Biology. [IF=1.281, Cited=15, 691060].
Case DA, Karplus M (1979) Dynamics of ligand binding to heme proteins. Journal of Molecular Biology. [IF=1.281,
Cited=182, 533895].
Northrup SH, Pear MR, Morgan JD, ..., Karplus M (1981) Molecular dynamics of ferrocytochrome c. Magnitude and anisotropy
of atomic displacements. Journal of Molecular Biology. [IF=1.281, Cited=61, 6283085].
Gelin BR, Lee AW, Karplus M (1983) Hemoglobin tertiary structural change on ligand binding. Its role in the co-operative
mechanism. Journal of Molecular Biology. [IF=1.281, Cited=67, 6663623].
Novotný J, Bruccoleri R, Karplus M (1984) An analysis of incorrectly folded protein models. Implications for structure
predictions. Journal of Molecular Biology. [IF=1.281, Cited=153, 6434748].
States DJ, Dobson CM, Dobson CM, ..., Karplus M (1984) A new two-disulphide intermediate in the refolding of reduced
bovine pancreatic trypsin inhibitor. Journal of Molecular Biology. [IF=1.281, Cited=37, 6201619].
Clore GM, Gronenborn AM, Brünger AT, Karplus M (1985) Solution conformation of a heptadecapeptide comprising the DNA
binding helix F of the cyclic AMP receptor protein of Escherichia coli. Combined use of 1H nuclear magnetic resonance
and restrained molecular dynamics. Journal of Molecular Biology. [IF=1.281, Cited=90, 3910844].
Chothia C, Novotný J, Bruccoleri R, Karplus M (1985) Domain association in immunoglobulin molecules. The packing of
variable domains. Journal of Molecular Biology. [IF=1.281, Cited=248, 4093982].
Post CB, Brooks BR, Karplus M, ..., Phillips DC (1986) Molecular dynamics simulations of native and substrate-bound
lysozyme. A study of the average structures and atomic fluctuations. Journal of Molecular Biology. [IF=1.281, Cited=55, 3783708].
Clore GM, Brünger AT, Karplus M, Gronenborn AM (1986) Application of molecular dynamics with interproton distance
restraints to three-dimensional protein structure determination. A model study of crambin. Journal of Molecular Biology.
[IF=1.281, Cited=113, 3029386].
Nilsson L, Clore GM, Gronenborn AM, ..., Karplus M (1986) Structure refinement of oligonucleotides by molecular dynamics
with nuclear Overhauser effect interproton distance restraints: application to 5' d(C-G-T-A-C-G)2. Journal of Molecular
Biology. [IF=1.281, Cited=49, 3016285].
Kuriyan J, Petsko GA, Levy RM, Karplus M (1986) Effect of anisotropy and anharmonicity on protein crystallographic
refinement. An evaluation by molecular dynamics. Journal of Molecular Biology. [IF=1.281, Cited=90, 3795269].
Kuriyan J, Wilz S, Karplus M, Petsko GA (1986) X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5
A resolution. Journal of Molecular Biology. [IF=1.281, Cited=186, 3820301].
States DJ, Creighton TE, Dobson CM, ..., Karplus M (1987) Conformations of intermediates in the folding of the
pancreatic trypsin inhibitor. Journal of Molecular Biology. [IF=1.281, Cited=50, 2443711].
Summers NL, Carlson WD, Karplus M (1987) Analysis of side-chain orientations in homologous proteins. Journal of
Molecular Biology. [IF=1.281, Cited=67, 3309349].
Delepierre M, Dobson CM, Dobson CM, ..., Wedin RE (1987) Electrostatic effects and hydrogen exchange behaviour in
proteins. The pH dependence of exchange rates in lysozyme. Journal of Molecular Biology. [IF=1.281, Cited=40, 2824793].
Bashford D, Karplus M, Canters GW (1988) Electrostatic effects of charge perturbations introduced by metal oxidation in
proteins. A theoretical analysis. Journal of Molecular Biology. [IF=1.281, Cited=22, 3199443].
Cusack S, Smith J, Finney J, ..., Karplus M (1988) Inelastic neutron scattering analysis of picosecond internal protein
dynamics. Comparison of harmonic theory with experiment. Journal of Molecular Biology. [IF=1.281, Cited=48, 2459399].
Brooks CL, Karplus M (1989) Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the
active site region of lysozyme. Journal of Molecular Biology. [IF=1.281, Cited=192, 2769750].
Summers NL, Karplus M (1989) Construction of side-chains in homology modelling. Application to the C-terminal lobe of
rhizopuspepsin. Journal of Molecular Biology. [IF=1.281, Cited=47, 2693742].
Lau FT, Karplus M (1994) Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA
synthetase mutant. Journal of Molecular Biology. [IF=1.281, Cited=23, 8120886].
Meizner I, Katz M, Leventhal H, ..., Insler V (1981) Cesarean section--a review of two annual periods separated by a
ten-year interval. European Journal of Obstetrics, Gynecology and Reproductive Biology. [IF=1.154, Cited=1, 7333411].
Insler V, Larholt K, Hagay ZJ, ..., Stone D (1986) The impact of prenatal care on the outcome of pregnancy. European
Journal of Obstetrics, Gynecology and Reproductive Biology. [IF=1.154, Cited=14, 3817263].
Karplus M (1984) Dynamics of proteins. None. [IF=None, Cited=14, 6100468].
Brooks CL, Karplus M (1986) Theoretical approaches to solvation of biopolymers. None. [IF=None, Cited=11, 3736426].
Karplus M (1986) Internal dynamics of proteins. None. [IF=None, Cited=24, 3773762].
Dobson CM, Dobson CM, Karplus M, Karplus M (1986) Internal motion of proteins: nuclear magnetic resonance measurements
and dynamic simulations. None. [IF=None, Cited=22, 3773766].
Summers NL, Karplus M (1991) Modeling of side chains, loops, and insertions in proteins. None. [IF=None, Cited=8, 1784173].
Holley LH, Karplus M (1991) Neural networks for protein structure prediction. None. [IF=None, Cited=14, 1784175].
Leiberman JR, Fraser D, Mazor M, ..., Glezerman M (1995) Breech presentation and cesarean section in term nulliparous
women. European Journal of Obstetrics, Gynecology and Reproductive Biology. [IF=1.154, Cited=9, 7556830].
Molteno C, Magasiner V, Sayed R, Karplus M (1990) Postural development in very low birth weight and normal birth weight
infants. Early Human Development. [IF=1.059, Cited=2, 2076690].
Zhou Y, Cook M, Karplus M (2000) Protein motions at zero-total angular momentum: the importance of long-range
correlations. Biophysical Journal. [IF=0.842, Cited=17, 11106598].
Paci E, Vendruscolo M, Karplus M (2002) Validity of Gō models: comparison with a solvent-shielded empirical energy
decomposition. Biophysical Journal. [IF=0.842, Cited=42, 12496075].
Reddy SY, Leclerc F, Karplus M (2003) DNA polymorphism: a comparison of force fields for nucleic acids. Biophysical
Journal. [IF=0.842, Cited=38, 12609851].
Meuwly M, Karplus M (2004) Theoretical investigations on Azotobacter vinelandii ferredoxin I: effects of electron
transfer on protein dynamics. Biophysical Journal. [IF=0.842, Cited=4, 15041642].
Karplus M, Gelin BR, McCammon JA (1980) Internal dynamics of proteins. Short time and long time motions of aromatic
sidechains in PTI. Biophysical Journal. [IF=0.842, Cited=14, 7248464].
Levy RM, Karplus M, McCammon JA (1980) Molecular dynamics studies of NMR relaxation in proteins. Biophysical Journal.
[IF=0.842, Cited=5, 19431400].
Levy RM, Dobson CM, Dobson CM, ..., Karplus M (1982) Dipolar NMR relaxation of nonprotonated aromatic carbons in
proteins. Structural and dynamical effects. Biophysical Journal. [IF=0.842, Cited=8, 6179550].
Levy RM, Sheridan RP, Keepers JW, ..., Karplus M (1985) Molecular dynamics of myoglobin at 298 degrees K. Results from a
300-ps computer simulation. Biophysical Journal. [IF=0.842, Cited=31, 3840041].
Weiss MA, Stearman R, Jeitler-Nilsson A, ..., Sauer RT (1986) Protein-Protein Interactions in DNA Recognition: H-NMR
Studies of Lambda cI Repressors Genetically Altered by Site-Directed Mutagenesis. Biophysical Journal. [IF=0.842,
Cited=0, 19431635].
Roux B, Karplus M (1988) The normal modes of the gramicidin-A dimer channel. Biophysical Journal. [IF=0.842, Cited=39, 2450595].
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Watanabe M, Rosenbusch J, Schirmer T, Karplus M (1997) Computer simulations of the OmpF porin from the outer membrane of
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Islam SA, Karplus M, Weaver DL (2002) Application of the diffusion-collision model to the folding of three-helix bundle
proteins. Journal of Molecular Biology. [IF=1.281, Cited=66, 12054779].
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Summers NL, Karplus M (1990) Modeling of globular proteins. A distance-based data search procedure for the construction
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Petrella RJ, Lazaridis T, Karplus M (1998) Protein sidechain conformer prediction: a test of the energy function. None.
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Spichty M, Taly A, Hagn F, ..., Karplus M (2009) The HSP90 binding mode of a radicicol-like E-oxime determined by
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Gao YQ, Yang W, Karplus M (2005) A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase. Cell.
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Cui Q, Li G, Ma J, Karplus M (2004) A normal mode analysis of structural plasticity in the biomolecular motor
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Zoete V, Meuwly M, Karplus M (2004) A comparison of the dynamic behavior of monomeric and dimeric insulin shows
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molecular dynamics simulation analysis. Journal of Molecular Biology. [IF=1.281, Cited=52, 15876377].
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of molecular symmetry. Journal of Molecular Biology. [IF=1.281, Cited=44, 15922356].
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folding rates. Journal of Molecular Biology. [IF=1.281, Cited=44, 16120445].
Maragakis P, Karplus M (2005) Large amplitude conformational change in proteins explored with a plastic network model:
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Kong Y, Ma J, Karplus M, Lipscomb WN (2005) The allosteric mechanism of yeast chorismate mutase: a dynamic analysis.
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Islam SA, Karplus M, Weaver DL (2004) The role of sequence and structure in protein folding kinetics; the diffusion-
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Kong Y, Karplus M (2007) The signaling pathway of rhodopsin. Structure. [IF=1.155, Cited=32, 17502106].
Hwang W, Lang MJ, Karplus M (2008) Force generation in kinesin hinges on cover-neck bundle formation. Structure.
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Komazin-Meredith G, Petrella RJ, Santos WL, ..., Coen DM (2008) The human cytomegalovirus UL44 C clamp wraps around DNA.
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Golosov AA, Warren JJ, Beese LS, Karplus M (2010) The mechanism of the translocation step in DNA replication by DNA
polymerase I: a computer simulation analysis. Structure. [IF=1.155, Cited=43, 20152155].
Cecchini M, Alexeev Y, Karplus M (2010) Pi release from myosin: a simulation analysis of possible pathways. Structure.
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Szabo A, Karplus M (1972) A mathematical model for structure-function relationships in hemoglobin. Biochemical and
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of Molecular Biology. [IF=1.281, Cited=116, 12270718].
Michielin O, Karplus M (2002) Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide
mutation: a simulation analysis. Journal of Molecular Biology. [IF=1.281, Cited=35, 12445788].
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Cui Q, Karplus M (2003) Catalysis and specificity in enzymes: a study of triosephosphate isomerase and comparison with
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Lazaridis T, Archontis G, Karplus M (1995) Enthalpic contribution to protein stability: insights from atom-based
calculations and statistical mechanics. None. [IF=None, Cited=62, 8561050].
Schaefer M, van Vlijmen HW, Karplus M (1998) Electrostatic contributions to molecular free energies in solution. None.
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Meuwly M, Becker OM, Stote R, Karplus M (2002) NO rebinding to myoglobin: a reactive molecular dynamics study.
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Lazaridis T, Karplus M (2000) Effective energy functions for protein structure prediction. Current Opinion in Structural
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experiment. Current Opinion in Structural Biology. [IF=1.4, Cited=196, 10047588].
Dinner AR, Sali A, Smith LJ, ..., Karplus M (2000) Understanding protein folding via free-energy surfaces from theory
and experiment. Trends in Biochemical Sciences. [IF=2.462, Cited=225, 10871884].
Ma J, Flynn TC, Cui Q, ..., Karplus M (2002) A dynamic analysis of the rotation mechanism for conformational change in
F(1)-ATPase. Structure. [IF=1.155, Cited=80, 12121647].
Dutzler R, Schirmer T, Karplus M, Fischer S (2002) Translocation mechanism of long sugar chains across the maltoporin
membrane channel. Structure. [IF=1.155, Cited=23, 12220498].
Caflisch A, Karplus M (1999) Structural details of urea binding to barnase: a molecular dynamics analysis. Structure.
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Fischer S, Michnick S, Karplus M (1993) A mechanism for rotamase catalysis by the FK506 binding protein (FKBP).
Biochemistry. [IF=0.753, Cited=54, 7505615].
Tidor B, Karplus M (1991) Simulation analysis of the stability mutant R96H of T4 lysozyme. Biochemistry. [IF=0.753,
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Petrich JW, Lambry JC, Kuczera K, ..., Martin JL (1991) Ligand binding and protein relaxation in heme proteins: a room
temperature analysis of NO geminate recombination. Biochemistry. [IF=0.753, Cited=66, 2018766].
Rosen MK, Michnick SW, Karplus M, Schreiber SL (1991) Proton and nitrogen sequential assignments and secondary structure
determination of the human FK506 and rapamycin binding protein. Biochemistry. [IF=0.753, Cited=21, 1709363].
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triosephosphate isomerase. Biochemistry. [IF=0.753, Cited=72, 2043624].
Swaminathan S, Ichiye T, van Gunsteren W, Karplus M (1982) Time dependence of atomic fluctuations in proteins: analysis
of local and collective motions in bovine pancreatic trypsin inhibitor. Biochemistry. [IF=0.753, Cited=70, 7171552].
Ichiye T, Karplus M (1983) Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study.
Biochemistry. [IF=0.753, Cited=63, 6871168].
Weiss MA, Sauer RT, Patel DJ, Karplus M (1984) Amino-terminal arm of the lambda repressor: a 1H NMR study. Biochemistry.
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Weiss MA, Pabo CO, Karplus M, Sauer RT (1987) Dimerization of the operator binding domain of phage lambda repressor.
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Nilges M, Clore GM, Gronenborn AM, ..., Nilsson L (1987) Refinement of the solution structure of the DNA hexamer
5'd(GCATGC)2: combined use of nuclear magnetic resonance and restrained molecular dynamics. Biochemistry. [IF=0.753,
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Brünger AT, Huber R, Karplus M (1987) Trypsinogen-trypsin transition: a molecular dynamics study of induced
conformational change in the activation domain. Biochemistry. [IF=0.753, Cited=25, 3663651].
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for the cooperative mechanism. Biochemistry. [IF=0.753, Cited=32, 2835088].
Ichiye T, Karplus M (1988) Anisotropy and anharmonicity of atomic fluctuations in proteins: implications for X-ray
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monomer: assignment of aromatic resonances with application to protein folding, structure, and dynamics. Biochemistry.
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Bashford D, Karplus M (1990) pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model.
Biochemistry. [IF=0.753, Cited=533, 2271649].
Hoch JC, Dobson CM, Dobson CM, ..., Karplus M (1982) Fluctuations and averaging of proton chemical shifts in the bovine
pancreatic trypsin inhibitor. Biochemistry. [IF=0.753, Cited=16, 6280757].
van Gunsteren WF, Karplus M (1982) Protein dynamics in solution and in a crystalline environment: a molecular dynamics
study. Biochemistry. [IF=0.753, Cited=88, 6178423].
McCammon JA, Wolynes PG, Karplus M (1979) Picosecond dynamics of tyrosine side chains in proteins. Biochemistry.
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Gelin BR, Karplus M (1979) Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment.
Biochemistry. [IF=0.753, Cited=131, 427111].
Szabo A, Karplus M (1976) Analysis of the interaction of organic phosphates with hemoglobin. Biochemistry. [IF=0.753,
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Szabo A, Karplus M (1975) Analysis of cooperativity in hemoglobin. Valency hybrids, oxidation, and methemoglobin
replacement reactions. Biochemistry. [IF=0.753, Cited=19, 235946].
Rowan R, Warshel A, Warshel A, ..., Karplus M (1974) Conformation of retinal isomers. Biochemistry. [IF=0.753,
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Huynh BH, Case DA, Karplus M (1977) Nature of the iron-oxygen bond in oxyhemoglobin. Journal of the American Chemical
Society. [IF=2.573, Cited=4, 893879].
Case DA, Karplus M (1977) Xalpha multiple scattering calculations on copper porphine. Journal of the American Chemical
Society. [IF=2.573, Cited=4, 197139].
Warshel A, Warshel A, Karplus M, Karplus M (1974) Calculation of pi-pi excited state conformations and vibronic
structure of retinal and related molecules. Journal of the American Chemical Society. [IF=2.573, Cited=36, 4412283].
Gelin BR, Karplus M (1975) Role of structural flexibility in conformational calculations. Application to acetylcholine
and beta-methylacetylcholine. Journal of the American Chemical Society. [IF=2.573, Cited=10, 1184892].
Caflisch A, Miranker A, Karplus M (1993) Multiple copy simultaneous search and construction of ligands in binding sites:
application to inhibitors of HIV-1 aspartic proteinase. Journal of Medicinal Chemistry. [IF=1.655, Cited=93, 8340918].
So SS, Karplus M (1999) A comparative study of ligand-receptor complex binding affinity prediction methods based on
glycogen phosphorylase inhibitors. Journal of Computer-Aided Molecular Design. [IF=0.881, Cited=24, 10216832].
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So SS, Karplus M (2001) Evaluation of designed ligands by a multiple screening method: application to glycogen
phosphorylase inhibitors constructed with a variety of approaches. Journal of Computer-Aided Molecular Design.
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Bitetti-Putzer R, Joseph-McCarthy D, Hogle JM, Karplus M (2001) Functional group placement in protein binding sites: a
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Zoete V, Michielin O, Karplus M (2003) Protein-ligand binding free energy estimation using molecular mechanics and
continuum electrostatics. Application to HIV-1 protease inhibitors. Journal of Computer-Aided Molecular Design.
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Honig B, Karplus M (1971) Implications of torsional potential of retinal isomers for visual excitation. Nature.
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Karplus M, Weaver DL (1976) Protein-folding dynamics. Nature. [IF=11.591, Cited=298, 1256583].
McCammon JA, Gelin BR, Karplus M, Wolynes PG (1976) The hinge-bending mode in lysozyme. Nature. [IF=11.591, Cited=160, 958384].
McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature. [IF=11.591, Cited=672, 301613].
McCammon JA, Karplus M (1977) Internal motions of antibody molecules. Nature. [IF=11.591, Cited=34, 895880].
Karplus M, McCammon JA (1979) Protein structural fluctuations during a period of 100 ps. Nature. [IF=11.591, Cited=60, 763343].
Northrup SH, Pear MR, McCammon JA, Karplus M (1980) Molecular dynamics of ferrocytochrome c. Nature. [IF=11.591,
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van Gunsteren WF, Karplus M (1981) Effect of constraints, solvent and crystal environment on protein dynamics. Nature.
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Miranker A, Radford SE, Karplus M, ..., Dobson CM (1991) Demonstration by NMR of folding domains in lysozyme. Nature.
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Vendruscolo M, Paci E, Dobson CM, ..., Karplus M (2001) Three key residues form a critical contact network in a protein
folding transition state. Nature. [IF=11.591, Cited=264, 11214326].
Dinner AR, Blackburn GM, Karplus M (2001) Uracil-DNA glycosylase acts by substrate autocatalysis. Nature. [IF=11.591,
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Zhou Y, Karplus M (1999) Interpreting the folding kinetics of helical proteins. Nature. [IF=11.591, Cited=131, 10517642].
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Dinner AR, Karplus M (2001) The roles of stability and contact order in determining protein folding rates. None.
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Banerjee A, Yang W, Karplus M, Verdine GL (2005) Structure of a repair enzyme interrogating undamaged DNA elucidates
recognition of damaged DNA. Nature. [IF=11.591, Cited=202, 15800616].
Henzler-Wildman KA, Lei M, Thai V, ..., Kern D (2007) A hierarchy of timescales in protein dynamics is linked to enzyme
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Vitkup D, Petsko GA, Karplus M (1997) A comparison between molecular dynamics and X-ray results for dissociated CO in
myoglobin. None. [IF=None, Cited=39, 9164461].
Dinner AR, Karplus M (1998) A metastable state in folding simulations of a protein model. None. [IF=None, Cited=16, 9501918].
Dunbrack RL, Karplus M (1994) Conformational analysis of the backbone-dependent rotamer preferences of protein
sidechains. None. [IF=None, Cited=175, 7664040].
Fromme JC, Bruner SD, Yang W, ..., Verdine GL (2003) Product-assisted catalysis in base-excision DNA repair. None.
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Karplus M, McCammon JA (1986) The dynamics of proteins. None. [IF=None, Cited=26, 2938253].
Shinwell ES, Sciaky Y, Karplus M (2002) Effect of position changing on bilirubin levels during phototherapy. Journal of
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Meuwly M, Karplus M (2003) Theoretical investigations of Ferredoxin I: the possible role of internal water molecules on
the coupled electron proton transfer reaction. None. [IF=None, Cited=6, 14527222].
Levene C, Sela R, Rudolphson Y, ..., Dvilansky A (1977) Hemolytic disease of the newborn due to anti-PP1 P k (anti-Tj
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Gelin BR, Karplus M (1975) Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic
trypsin inhibitor. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765,
Cited=90, 1056008].
Gelin BR, Karplus M (1977) Mechanism of tertiary structural change in hemoglobin. Proceedings of the National Academy of
Sciences of the United States of America. [IF=2.765, Cited=66, 265575].
McCammon JA, Karplus M (1979) Dynamics of activated processes in globular proteins. Proceedings of the National Academy
of Sciences of the United States of America. [IF=2.765, Cited=35, 291026].
Northrup SH, Pear MR, Lee CY, ..., Karplus M (1982) Dynamical theory of activated processes in globular proteins.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=60, 6955788].
Brooks B, Karplus M (1983) Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin
inhibitor. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=415, 6579545].
Lee AW, Karplus M (1983) Structure-specific model of hemoglobin cooperativity. Proceedings of the National Academy of
Sciences of the United States of America. [IF=2.765, Cited=33, 6580628].
Weiss MA, Patel DJ, Sauer RT, Karplus M (1984) Two-dimensional 1H NMR study of the lambda operator site OL1: a
sequential assignment strategy and its application. Proceedings of the National Academy of Sciences of the United States
of America. [IF=2.765, Cited=48, 6229791].
Brooks B, Karplus M (1985) Normal modes for specific motions of macromolecules: application to the hinge-bending mode of
lysozyme. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=174, 3860838].
Brünger AT, Brooks CL, Karplus M (1985) Active site dynamics of ribonuclease. Proceedings of the National Academy of
Sciences of the United States of America. [IF=2.765, Cited=68, 3866234].
Shih HH, Brady J, Karplus M (1985) Structure of proteins with single-site mutations: a minimum perturbation approach.
Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=26, 3856851].
Brünger AT, Clore GM, Gronenborn AM, Karplus M (1986) Three-dimensional structure of proteins determined by molecular
dynamics with interproton distance restraints: application to crambin. Proceedings of the National Academy of Sciences
of the United States of America. [IF=2.765, Cited=130, 3459158].
Matsumoto R, Sali A, Ghildyal N, ..., Stevens RL (1995) Packaging of proteases and proteoglycans in the granules of mast
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Weiss MA, Karplus M, Patel DJ, Sauer RT (1983) Solution NMR studies of intact lambda repressor. Journal of Biomolecular
Structure and Dynamics. [IF=1.22, Cited=11, 6401108].
Tidor B, Irikura KK, Brooks BR, Karplus M (1983) Dynamics of DNA oligomers. Journal of Biomolecular Structure and
Dynamics. [IF=1.22, Cited=90, 6400872].
Bashford D, Weaver DL, Karplus M (1984) Diffusion-collision model for the folding kinetics of the lambda-repressor
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Weiss MA, Karplus M, Sauer RT (1987) Quaternary structure and function in phage lambda repressor: 1H-NMR studies of
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Weiss MA, Patel DJ, Sauer RT, Karplus M (1984) 1H-NMR study of the lambda operator site OL1: assignment of the imino and
adenine H2 resonances. Nucleic Acids Research. [IF=4.663, Cited=14, 6233536].
Brünger AT, Clore GM, Gronenborn AM, Karplus M (1987) Solution conformations of human growth hormone releasing factor:
comparison of the restrained molecular dynamics and distance geometry methods for a system without long-range distance
data. None. [IF=None, Cited=31, 2854259].
Dinner AR, Verosub E, Karplus M (1999) Use of a quantitative structure-property relationship to design larger model
proteins that fold rapidly. None. [IF=None, Cited=3, 10585496].
Straub JE, Karplus M (1990) The interpretation of site-directed mutagenesis experiments by linear free energy relations.
None. [IF=None, Cited=4, 2217141].
Prod'hom B, Karplus M (1993) The nature of the ion binding interactions in EF-hand peptide analogs: free energy
simulation of Asp to Asn mutations. None. [IF=None, Cited=9, 8234229].
Joseph-McCarthy D, Petsko GA, Karplus M (1995) Use of a minimum perturbation approach to predict TIM mutant structures.
None. [IF=None, Cited=5, 8819976].
Carlson WD, Handschumacher M, Summers N, ..., Haber E (1987) Models for the three-dimensional structure of renin
inhibitors bound in the active site of human renin: an analysis of the properties that produce tight binding. Journal of
Cardiovascular Pharmacology. [IF=0.686, Cited=1, 2485071].
Gazala E, Karplus M, Liberman JR, Sarov I (1985) The effect of maternal measles on the fetus. None. [IF=None, Cited=2, 3982983].
Yagupsky P, Dagan R, Chipman M, ..., Karplus M (1991) Pseudooutbreak of Candida guilliermondii fungemia in a neonatal
intensive care unit. Pediatric Infectious Disease Journal. [IF=0.964, Cited=15, 1766709].
Vendruscolo M, Dokholyan NV, Paci E, Karplus M (2002) Small-world view of the amino acids that play a key role in
protein folding. None. [IF=None, Cited=144, 12188762].
Chekmarev SF, Palyanov AY, Karplus M (2008) Hydrodynamic description of protein folding. Physical Review Letters.
[IF=2.288, Cited=13, 18232827].
Elber R, Karplus M (1986) Low-frequency modes in proteins: Use of the effective-medium approximation to interpret the
fractal dimension observed in electron-spin relaxation measurements. Physical Review Letters. [IF=2.288, Cited=34, 10033176].
Shakhnovich E, Farztdinov G, Gutin A, Karplus M (1991) Protein folding bottlenecks: A lattice Monte Carlo simulation.
Physical Review Letters. [IF=2.288, Cited=125, 10044213].
Becker O, Karplus M (1993) Temperature echoes in molecular dynamics simulations of proteins. Physical Review Letters.
[IF=2.288, Cited=7, 10053888].
Zhou Y, Hall C, Karplus M (1996) First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model. Physical
Review Letters. [IF=2.288, Cited=66, 10062054].
Krivov SV, Chekmarev SF, Karplus M (2002) Potential energy surfaces and conformational transitions in biomolecules: a
successive confinement approach applied to a solvated tetrapeptide. Physical Review Letters. [IF=2.288, Cited=14, 11801090].
Maragakis P, Spichty M, Karplus M (2006) Optimal estimates of free energies from multistate nonequilibrium work data.
Physical Review Letters. [IF=2.288, Cited=31, 16605720].
Auer S, Miller MA, Krivov SV, ..., Vendruscolo M (2007) Importance of metastable states in the free energy landscapes of
polypeptide chains. Physical Review Letters. [IF=2.288, Cited=25, 17995375].
Ruiz F, Hazemann I, Mitschler A, ..., Podjarny A (2004) The crystallographic structure of the aldose reductase-IDD552
complex shows direct proton donation from tyrosine 48. None. [IF=None, Cited=13, 15272156].
Kuriyan J, Brünger AT, Karplus M, Hendrickson WA (1989) X-ray refinement of protein structures by simulated annealing:
test of the method on myohemerythrin. None. [IF=None, Cited=22, 2619971].
Cohen A, Cohen AE, Gutnick MJ, ..., Karplus M (1982) On quantitative analysis of periodicity in neonatal respiratory
signals. IEEE Transactions on Biomedical Engineering. [IF=1.611, Cited=0, 7106801].
Cui Q, Karplus M (2008) Allostery and cooperativity revisited. Protein Science. [IF=1.97, Cited=355, 18560010].
Zhou Y, Hall CK, Karplus M (1999) The calorimetric criterion for a two-state process revisited. Protein Science.
[IF=1.97, Cited=49, 10338017].
Yagupsky P, Reuveni H, Karplus M, Moses S (1986) Aplasia cutis congenita in one of monozygotic twins. Pediatric
Dermatology. [IF=0.814, Cited=2, 3809026].
Karplus M (1981) Aspects of protein dynamics. Annals of the New York Academy of Sciences. [IF=1.878, Cited=6, 6942760].
Karplus M (1986) Molecular dynamics: applications to proteins. Annals of the New York Academy of Sciences. [IF=1.878,
Cited=2, 3471110].
Evenson JW, Karplus M (1993) Effective coupling in biological electron transfer: exponential or complex distance
dependence? Science. [IF=7.729, Cited=20, 8235654].
Shinwell ES, Karplus M, Zmora E, ..., Gottfried S (1996) Failure of early postnatal dexamethasone to prevent chronic
lung disease in infants with respiratory distress syndrome. Archives of Disease in Childhood: Fetal and Neonatal
Edition. [IF=2.227, Cited=43, 8653433].
Shinwell ES, Karplus M, Reich D, ..., Gottfried E (2000) Early postnatal dexamethasone treatment and increased incidence
of cerebral palsy. Archives of Disease in Childhood: Fetal and Neonatal Edition. [IF=2.227, Cited=181, 11040164].
Shinwell ES, Karplus M, Bader D, ..., Kohelet D (2003) Neonatologists are using much less dexamethasone. Archives of
Disease in Childhood: Fetal and Neonatal Edition. [IF=2.227, Cited=15, 12937052].
Roux B, Karplus M (1994) Molecular dynamics simulations of the gramicidin channel. None. [IF=None, Cited=97, 7522667].
Karplus M, McCammon JA (1983) Dynamics of proteins: elements and function. Annual Review of Biochemistry. [IF=5.273,
Cited=272, 6351724].
Agam G, Deutsch I, Karplus M, Livne AA (1993) Erythrocyte Li+i-Na+o countertransport in the newborn. None. [IF=None,
Cited=0, 8399795].
Carlson W, Karplus M, Haber E (1985) Construction of a model for the three-dimensional structure of human renal renin.
Hypertension. [IF=2.252, Cited=39, 3884498].
Levinson NM, Kuchment O, Shen K, ..., Kuriyan J (2006) A Src-like inactive conformation in the abl tyrosine kinase
domain. PLoS Biology. [IF=2.285, Cited=182, 16640460].
Cecchini M, Houdusse A, Karplus M (2008) Allosteric communication in myosin V: from small conformational changes to
large directed movements. PLoS Computational Biology. [IF=1.278, Cited=56, 18704171].
van der Vaart A, Ma J, Karplus M (2004) The unfolding action of GroEL on a protein substrate. Biophysical Journal.
[IF=0.842, Cited=32, 15240489].
Andricioaei I, Goel A, Herschbach D, Karplus M (2004) Dependence of DNA polymerase replication rate on external forces:
a model based on molecular dynamics simulations. Biophysical Journal. [IF=0.842, Cited=14, 15345530].
Adamovic I, Mijailovich SM, Karplus M (2008) The elastic properties of the structurally characterized myosin II S2
subdomain: a molecular dynamics and normal mode analysis. Biophysical Journal. [IF=0.842, Cited=47, 18234833].
Karplus M, McCammon JA (1981) The internal dynamics of globular proteins. None. [IF=None, Cited=201, 7009056].
Friling R, Rosen SD, Monos T, ..., Yassur Y (1997) Retinopathy of prematurity in multiple-gestation, very low birth
weight infants. Journal of Pediatric Ophthalmology and Strabismus. [IF=0.705, Cited=22, 9083954].
Chandonia JM, Karplus M (1999) New methods for accurate prediction of protein secondary structure. Proteins: Structure,
Function and Bioinformatics. [IF=0.897, Cited=54, 10328264].
Stultz CM, Karplus M (1999) MCSS functionality maps for a flexible protein. Proteins: Structure, Function and
Bioinformatics. [IF=0.897, Cited=19, 10651268].
Stultz CM, Karplus M (2000) Dynamic ligand design and combinatorial optimization: designing inhibitors to
endothiapepsin. Proteins: Structure, Function and Bioinformatics. [IF=0.897, Cited=16, 10842341].
Martí-Renom MA, Stote RH, Querol E, ..., Karplus M (2000) Structures of scrambled disulfide forms of the potato
carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints. Proteins: Structure, Function
and Bioinformatics. [IF=0.897, Cited=4, 10861940].
Shinwell ES, Zmora E, Leven D, ..., Karplus M (1992) [Surfactant replacement therapy for respiratory distress syndrome:
a pilot study]. None. [IF=None, Cited=1, 1505835].
Colonna-Cesari F, Perahia D, Karplus M, ..., Tapia O (1986) Interdomain motion in liver alcohol dehydrogenase.
Structural and energetic analysis of the hinge bending mode. Journal of Biological Chemistry. [IF=1.122, Cited=76, 3771574].
Rickham PP, Karplus M (1971) Familial and hereditary intestinal atresia. None. [IF=None, Cited=10, 5142939].
Karplus M (1971) [Endrin poisoning in children]. None. [IF=None, Cited=0, 5158977].
Dagon R, Karplus M, Maresh A, Bar-Ziv J (1979) [Congenital small left colon syndrome]. None. [IF=None, Cited=0, 520906].
Leiberman A, Brenner H, Karplus M, ..., Bar-Ziv J (1979) [Rare causes for laryngeal obstruction in infants]. None.
[IF=None, Cited=0, 520929].
Carlson W, Handschumacher M, Karplus M, Haber E (1984) Studies of the three-dimensional structure of human renin and its
inhibitors. None. [IF=None, Cited=0, 6400375].
Karplus M, Swaminathan S, Ichiye T, Van Gunsteren WF (1983) Local and collective motions in protein dynamics. None.
[IF=None, Cited=3, 6551229].
Novotný J, Bruccoleri R, Newell J, ..., Karplus M (1983) Molecular anatomy of the antibody binding site. Journal of
Biological Chemistry. [IF=1.122, Cited=66, 6643494].
Bar-Ziv J, Yagupsky P, Karplus M, ..., Maor E (1982) Congenital ulcerative colitis. None. [IF=None, Cited=1, 7065611].
Gradus D, Le Roith D, Karplus M, ..., Bar-Ziv J (1981) Congenital hyperparathyroidism and rickets: secondary to maternal
hypoparathyroidism and vitamin D deficiency. None. [IF=None, Cited=10, 7197265].
Sali A, Matsumoto R, McNeil HP, ..., Stevens RL (1993) Three-dimensional models of four mouse mast cell chymases.
Identification of proteoglycan binding regions and protease-specific antigenic epitopes. Journal of Biological
Chemistry. [IF=1.122, Cited=54, 7682557].
Monos T, Rosen SD, Karplus M, Yassur Y (1996) Fundus pigmentation in retinopathy of prematurity. Pediatrics. [IF=2.905,
Cited=9, 8604267].
Phillip M, De Boer C, Pilpel D, ..., Sofer S (1996) Clitoral and penile sizes of full term newborns in two different
ethnic groups. Journal of Pediatric Endocrinology and Metabolism. [IF=0.624, Cited=24, 8887140].

Karplus, Martin

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