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Martin Karplus

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

Research Profile (preview)

Concepts & Ideas

Occupations

Thermodynamics

Activities & Behaviors

Computer Simulation

Physiology

Protein Folding

Chemicals & Drugs

Phenomena

Procedures

X-Ray Crystallography

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Network (preview)

Co-Publications
Name
10
Krivov, Sergei
9
Ma, Jianpeng
7
Lazaridis, T
7
So, SS
7
Zoete, Vincent
6
Chekmarev, Sergei
6
Yang, Wei
6
Gao, Yi Qin
5
Dinner, Aaron
4
Cui, Qiang
4
Lipscomb, William
4
Meuwly, Markus
4
Zhou, Yaoqi
4
Archontis, Georgios
3
Simonson, Thomas

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Publications

TOP 3
Kalgin Igor V; Karplus Martin; Chekmarev Sergei F
Folding of a SH3 domain: standard and "hydrodynamic" analyses.
Spichty Martin; Taly Antoine; Hagn Franz; Kessler Horst; Barluenga Sofia; Winssinger Nicolas; Karplus Martin
The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15N chemical shifts.
Cecchini M; Krivov S V; Spichty M; Karplus M
Calculation of free-energy differences by confinement simulations. Application to peptide conformers.

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All Publications

2009: Kalgin Igor V; Karplus Martin; Chekmarev Sergei F
Folding of a SH3 domain: standard and "hydrodynamic" analyses.
The journal of physical chemistry. B 2009;113(38):12759-72.
2009: Spichty Martin; Taly Antoine; Hagn Franz; Kessler Horst; Barluenga Sofia; Winssinger Nicolas; Karplus Martin
The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15N chemical shifts.
Biophysical chemistry 2009;143(3):111-23.
2009: Cecchini M; Krivov S V; Spichty M; Karplus M
Calculation of free-energy differences by confinement simulations. Application to peptide conformers.
The journal of physical chemistry. B 2009;113(29):9728-40.
2009: Maragakis Paul; van der Vaart Arjan; Karplus Martin
Gaussian-mixture umbrella sampling.
The journal of physical chemistry. B 2009;113(14):4664-73.
2008: Krivov Sergei V; Karplus Martin
Diffusive reaction dynamics on invariant free energy profiles.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(37):13841-6.
2008: Maragakis Paul; Ritort Felix; Bustamante Carlos; Karplus Martin; Crooks Gavin E
Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise.
The Journal of chemical physics 2008;129(2):024102.
2008: Krivov Sergei V; Muff Stefanie; Caflisch Amedeo; Karplus Martin
One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process.
The journal of physical chemistry. B 2008;112(29):8701-14.
2008: Maragakis Paul; Spichty Martin; Karplus Martin
A differential fluctuation theorem.
The journal of physical chemistry. B 2008;112(19):6168-74.
2008: Chekmarev Sergei F; Palyanov Andrey Yu; Karplus Martin
Hydrodynamic description of protein folding.
Physical review letters 2008;100(1):018107.
2008: Pu Jingzhi; Karplus Martin
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 2008;105(4):1192-7.
2008: Cecchini M; Houdusse A; Karplus M
Allosteric communication in myosin V: from small conformational changes to large directed movements.
PLoS computational biology 2008;4(8):e1000129.
2007: Auer Stefan; Miller Mark A; Krivov Sergei V; Dobson Christopher M; Karplus Martin; Vendruscolo Michele
Importance of metastable states in the free energy landscapes of polypeptide chains.
Physical review letters 2007;99(17):178104.
2007: Kong Yifei; Karplus Martin
The signaling pathway of rhodopsin.
Structure (London, England : 1993) 2007;15(5):611-23.
2007: Wu Yudong; Gao Yi Qin; Karplus Martin
A kinetic model of coordinated myosin V.
Biochemistry 2007;46(21):6318-30.
2007: van der Vaart Arjan; Karplus Martin
Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.
The Journal of chemical physics 2007;126(16):164106.
2007: Palyanov Andrey Yu; Krivov Sergei V; Karplus Martin; Chekmarev Sergei F
A lattice protein with an amyloidogenic latent state: stability and folding kinetics.
The journal of physical chemistry. B 2007;111(10):2675-87.
2007: Golosov Andrei A; Karplus Martin
Probing polar solvation dynamics in proteins: a molecular dynamics simulation analysis.
The journal of physical chemistry. B 2007;111(6):1482-90.
2006: Krivov Sergei V; Karplus Martin
One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers.
The journal of physical chemistry. B 2006;110(25):12689-98.
2006: Bitetti-Putzer Ryan; Dinner Aaron R; Yang Wei; Karplus Martin
Conformational sampling via a self-regulating effective energy surface.
The Journal of chemical physics 2006;124(17):174901.
2006: Luo Guobin; Andricioaei Ioan; Xie X Sunney; Karplus Martin
Dynamic distance disorder in proteins is caused by trapping.
The journal of physical chemistry. B 2006;110(19):9363-7.
2006: Chekmarev Sergei F; Krivov Sergei V; Karplus Martin
Folding of ubiquitin: a simple model describes the strange kinetics.
The journal of physical chemistry. B 2006;110(17):8865-9.
2006: Maragakis Paul; Spichty Martin; Karplus Martin
Optimal estimates of free energies from multistate nonequilibrium work data.
Physical review letters 2006;96(10):100602.
2006: Kong Yifei; Ma Jianpeng; Karplus Martin; Lipscomb William N
The allosteric mechanism of yeast chorismate mutase: a dynamic analysis.
Journal of molecular biology 2006;356(1):237-47.
2006: Karplus Martin
Spinach on the ceiling: a theoretical chemist's return to biology.
Annual review of biophysics and biomolecular structure 2006;35():1-47.
2005: Archontis G; Watson K A; Xie Q; Andreou G; Chrysina E D; Zographos S E; Oikonomakos N G; Karplus M
Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues.
Proteins 2005;61(4):984-98.
2005: Gao Yi Qin; Yang Wei; Karplus Martin
A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase.
Cell 2005;123(2):195-205.
2005: Zoete Vincent; Meuwly Markus; Karplus Martin
Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition.
Proteins 2005;61(1):79-93.
2005: Maragakis Paul; Karplus Martin
Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase.
Journal of molecular biology 2005;352(4):807-22.
2005: Petrella Robert J; Karplus Martin
Electrostatic energies and forces computed without explicit interparticle interactions: a linear time complexity formulation.
Journal of computational chemistry 2005;26(8):755-87.
2005: Moulin Emilie; Zoete Vincent; Barluenga Sofia; Karplus Martin; Winssinger Nicolas
Design, synthesis, and biological evaluation of HSP90 inhibitors based on conformational analysis of radicicol and its analogues.
Journal of the American Chemical Society 2005;127(19):6999-7004.
2005: Karplus M; Kuriyan J
Molecular dynamics and protein function.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(19):6679-85.
2005: Chekmarev Sergei F; Krivov Sergei V; Karplus Martin
Folding time distributions as an approach to protein folding kinetics.
The journal of physical chemistry. B 2005;109(11):5312-30.
2005: van der Vaart Arjan; Karplus Martin
Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method.
The Journal of chemical physics 2005;122(11):114903.
2005: Banerjee Anirban; Yang Wei; Karplus Martin; Verdine Gregory L
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.
Nature 2005;434(7033):612-8.
2005: Karplus Martin; Gao Yi Qin; Ma Jianpeng; van der Vaart Arjan; Yang Wei
Protein structural transitions and their functional role.
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 2005;363(1827):331-55; discussion 355-6.
2004: Wan Shunzhou; Stote Roland H; Karplus Martin
Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes.
The Journal of chemical physics 2004;121(19):9539-48.
2004: Krivov Sergei V; Karplus Martin
Hidden complexity of free energy surfaces for peptide (protein) folding.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(41):14766-70.
2004: Andricioaei Ioan; Goel Anita; Herschbach Dudley; Karplus Martin
Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations.
Biophysical journal 2004;87(3):1478-97.
2004: Zoete Vincent; Meuwly Markus; Karplus Martin
A comparison of the dynamic behavior of monomeric and dimeric insulin shows structural rearrangements in the active monomer.
Journal of molecular biology 2004;342(3):913-29.
2004: van der Vaart Arjan; Ma Jianpeng; Karplus Martin
The unfolding action of GroEL on a protein substrate.
Biophysical journal 2004;87(1):562-73.
2004: Yang Wei; Bitetti-Putzer Ryan; Karplus Martin
Chaperoned alchemical free energy simulations: a general method for QM, MM, and QM/MM potentials.
The Journal of chemical physics 2004;120(20):9450-3.
2004: Zoete Vincent; Meuwly Markus; Karplus Martin
Investigation of glucose binding sites on insulin.
Proteins 2004;55(3):568-81.
2004: Karplus Martin; Gao Yi Qin
Biomolecular motors: the F1-ATPase paradigm.
Current opinion in structural biology 2004;14(2):250-9.
2004: Petrella Robert J; Karplus Martin
The role of carbon-donor hydrogen bonds in stabilizing tryptophan conformations.
Proteins 2004;54(4):716-26.
2004: Yang Wei; Bitetti-Putzer Ryan; Karplus Martin
Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence.
The Journal of chemical physics 2004;120(6):2618-28.
2003: Zoete V; Michielin O; Karplus M
Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors.
Journal of computer-aided molecular design 2003;17(12):861-80.
2003: Gao Yi Qin; Yang Wei; Marcus Rudolph A; Karplus Martin
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 2003;100(20):11339-44.
2003: Guo Hong; Cui Qiang; Lipscomb William N; Karplus Martin
Understanding the role of active-site residues in chorismate mutase catalysis from molecular-dynamics simulations.
Angewandte Chemie (International ed. in English) 2003;42(13):1508-11.
2003: Reddy Swarnalatha Y; Leclerc Fabrice; Karplus Martin
DNA polymorphism: a comparison of force fields for nucleic acids.
Biophysical journal 2003;84(3):1421-49.
2003: Karplus Martin
Molecular dynamics of biological macromolecules: a brief history and perspective.
Biopolymers 2003;68(3):350-8.
2003: Zhou Yaoqi; Zhou Hongyi; Karplus Martin
Cooperativity in Scapharca dimeric hemoglobin: simulation of binding intermediates and elucidation of the role of interfacial water.
Journal of molecular biology 2003;326(2):593-606.
2003: Yang W; Gao Y Q; Cui Q; Ma J; Karplus M
The missing link between thermodynamics and structure in F1-ATPase.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(3):874-9.
2003: Petrella Robert J; Andricioaei Ioan; Brooks Bernard R; Karplus Martin
An improved method for nonbonded list generation: rapid determination of near-neighbor pairs.
Journal of computational chemistry 2003;24(2):222-31.
2002: Paci Emanuele; Vendruscolo Michele; Karplus Martin
Validity of Go models: comparison with a solvent-shielded empirical energy decomposition.
Biophysical journal 2002;83(6):3032-8.
2002: Paci Emanuelel; Vendruscolo Michele; Dobson Christopher M; Karplus Martin
Determination of a transition state at atomic resolution from protein engineering data.
Journal of molecular biology 2002;324(1):151-63.
2002: Michielin Olivier; Zoete Vincent; Gierasch Tiffany Malinky; Eckstein Jens; Napper Andrew; Verdine Gregory; Karplus Martin
Conformational analysis of a stereochemically complete set of cis-enediol peptide analogues.
Journal of the American Chemical Society 2002;124(37):11131-41.
2002: Karplus Martin; McCammon J Andrew
Molecular dynamics simulations of biomolecules.
Nature structural biology 2002;9(9):646-52.
2002: Meuwly Markus; Becker Oren M; Stote Roland; Karplus Martin
NO rebinding to myoglobin: a reactive molecular dynamics study.
Biophysical chemistry 2002;98(1-2):183-207.
2002: Simonson Thomas; Archontis Georgios; Karplus Martin
Free energy simulations come of age: protein-ligand recognition.
Accounts of chemical research 2002;35(6):430-7.
2002: Cui Qiang; Karplus Martin
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 2002;124(12):3093-124.
2002: Krivov Sergei V; Chekmarev Sergei F; Karplus Martin
Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide.
Physical review letters 2002;88(3):038101.
2002: Zoete V; Michielin O; Karplus M
Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.
Journal of molecular biology 2002;315(1):21-52.
2001: Paci E; Caflisch A; Plückthun A; Karplus M
Forces and energetics of hapten-antibody dissociation: a biased molecular dynamics simulation study.
Journal of molecular biology 2001;314(3):589-605.
2001: Petrella R J; Karplus M
The energetics of off-rotamer protein side-chain conformations.
Journal of molecular biology 2001;312(5):1161-75.
2001: So S S; Karplus M
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 2001;15(7):613-47.
2001: Guo H; Cui Q; Lipscomb W N; Karplus M
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 2001;98(16):9032-7.
2001: Archontis G; Simonson T; Karplus M
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 2001;306(2):307-27.
2000: Zhou Y; Cook M; Karplus M
Protein motions at zero-total angular momentum: the importance of long-range correlations.
Biophysical journal 2000;79(6):2902-8.
2000: Ma J; Sigler P B; Xu Z; Karplus M
A dynamic model for the allosteric mechanism of GroEL.
Journal of molecular biology 2000;302(2):303-13.
2000: Stultz C M; Karplus M
Dynamic ligand design and combinatorial optimization: designing inhibitors to endothiapepsin.
Proteins 2000;40(2):258-89.
2000: Paci E; Karplus M
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 2000;97(12):6521-6.
2000: So S S; van Helden S P; van Geerestein V J; Karplus M
Quantitative structure-activity relationship studies of progesterone receptor binding steroids.
Journal of chemical information and computer sciences 2000;40(3):762-72.
1999: Stultz C M; Karplus M
MCSS functionality maps for a flexible protein.
Proteins 1999;37(4):512-29.
1999: Zhou Y; Karplus M
Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis.
Journal of molecular biology 1999;293(4):917-51.
1999: Zhou Y; Karplus M
Interpreting the folding kinetics of helical proteins.
Nature 1999;401(6751):400-3.
1999: Blondel A; Renaud J P; Fischer S; Moras D; Karplus M
Retinoic acid receptor: a simulation analysis of retinoic acid binding and the resulting conformational changes.
Journal of molecular biology 1999;291(1):101-15.
1999: Dinner A R; Lazaridis T; Karplus M
Understanding beta-hairpin formation.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(16):9068-73.
1999: Zhou Y; Hall C K; Karplus M
The calorimetric criterion for a two-state process revisited.
Protein science : a publication of the Protein Society 1999;8(5):1064-74.
1999: Lazaridis T; Karplus M
Discrimination of the native from misfolded protein models with an energy function including implicit solvation.
Journal of molecular biology 1999;288(3):477-87.
1999: Paci E; Karplus M
Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations.
Journal of molecular biology 1999;288(3):441-59.
1999: Lazaridis T; Karplus M
Effective energy function for proteins in solution.
Proteins 1999;35(2):133-52.
1999: So S S; Karplus M
A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors.
Journal of computer-aided molecular design 1999;13(3):243-58.
1999: Lazaridis T; Karplus M
Heat capacity and compactness of denatured proteins.
Biophysical chemistry 1999;78(1-2):207-17.
1999: Dinner A R; Abkevich V; Shakhnovich E; Karplus M
Factors that affect the folding ability of proteins.
Proteins 1999;35(1):34-40.
1999: Karplus M; Janin J
Comment on: 'The entropy cost of protein association'.
Protein engineering 1999;12(3):185-6; discussion 187.
1999: Zhou Y; Vitkup D; Karplus M
Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state.
Journal of molecular biology 1999;285(4):1371-5.
1998: Bartels C; Stote R H; Karplus M
Characterization of flexible molecules in solution: the RGDW peptide.
Journal of molecular biology 1998;284(5):1641-60.
1998: Ma J; Zheng X; Schnappauf G; Braus G; Karplus M; Lipscomb W N
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 1998;95(25):14640-5.
1998: Dinner A R; So S S; Karplus M
Use of quantitative structure-property relationships to predict the folding ability of model proteins.
Proteins 1998;33(2):177-203.
1998: van Vlijmen H W; Schaefer M; Karplus M
Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure.
Proteins 1998;33(2):145-58.
1998: Ma J; Karplus M
The allosteric mechanism of the chaperonin GroEL: a dynamic analysis.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(15):8502-7.
1998: Dinner A R; Karplus M
A metastable state in folding simulations of a protein model.
Nature structural biology 1998;5(3):236-41.
1998: Archontis G; Simonson T; Moras D; Karplus M
Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations.
Journal of molecular biology 1998;275(5):823-46.
1998: van Vlijmen H W; Curry S; Schaefer M; Karplus M
Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH.
Journal of molecular biology 1998;275(2):295-308.
1998: Petrella R J; Lazaridis T; Karplus M
Protein sidechain conformer prediction: a test of the energy function.
Folding & design 1998;3(5):353-77.
1997: So S S; Karplus M
Three-dimensional quantitative structure-activity relationships from molecular similarity matrices and genetic neural networks. 2. Applications.
Journal of medicinal chemistry 1997;40(26):4360-71.
1997: So S S; Karplus M
Three-dimensional quantitative structure-activity relationships from molecular similarity matrices and genetic neural networks. 1. Method and validations.
Journal of medicinal chemistry 1997;40(26):4347-59.
1997: Lazaridis T; Lee I; Karplus M
Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin.
Protein science : a publication of the Protein Society 1997;6(12):2589-605.
1997: Zhou Y; Karplus M
Folding thermodynamics of a model three-helix-bundle protein.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(26):14429-32.
1997: Lazaridis T; Karplus M
"New view" of protein folding reconciled with the old through multiple unfolding simulations.
Science (New York, N.Y.) 1997;278(5345):1928-31.
1997: Ma J; Karplus M
Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis.
Journal of molecular biology 1997;274(1):114-31.
1997: Ma J; Karplus M
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 1997;94(22):11905-10.
1997: Watanabe M; Rosenbusch J; Schirmer T; Karplus M
Computer simulations of the OmpF porin from the outer membrane of Escherichia coli.
Biophysical journal 1997;72(5):2094-102.
1997: van Vlijmen H W; Karplus M
PDB-based protein loop prediction: parameters for selection and methods for optimization.
Journal of molecular biology 1997;267(4):975-1001.
1997: Karplus M
The Levinthal paradox: yesterday and today.
Folding & design 1997;2(4):S69-75.
1996: So S S; Karplus M
Genetic neural networks for quantitative structure-activity relationships: improvements and application of benzodiazepine affinity for benzodiazepine/GABAA receptors.
Journal of medicinal chemistry 1996;39(26):5246-56.

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