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Author Details

Martin Karplus
Harvard University
1959
439
117
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36346605A Computational Framework for Determining the Breadth of Antibodies Against Highly Mutable Pathogens.Methods Mol Biol2023
37756691Free Energy Simulations of Receptor-Binding Domain Opening of the SARS-CoV-2 Spike Indicate a Barrierless Transition with Slow Conformational Motions.J Phys Chem B2023
36641390Water dynamics around T<sub>0</sub> vs R<sub>4</sub> of hemoglobin from local hydrophobicity analysis.J Chem Phys2023
34756740The functional role of the hemoglobin-water interface.Mol Aspects Med2022
35371013A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance.Front Immunol2022
35930347ppdx: Automated modeling of protein-protein interaction descriptors for use with machine learning.J Comput Chem2022
35298819Molecular Simulation of Stapled Peptides.Methods Mol Biol2022
33637649Design of immunogens to elicit broadly neutralizing antibodies against HIV targeting the CD4 binding site.Proc Natl Acad Sci U S A2021
32895378The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase.Nat Commun2020
32045240Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model.J Chem Theory Comput2020
33003727A restrained locally enhanced sampling method (RLES) for finding free energy minima in complex systems.J Chem Phys2020
32589026Water Dynamics Around Proteins: T- and R-States of Hemoglobin and Melittin.J Phys Chem B2020
30970017Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning.PLoS Comput Biol2019
31341091Insights into the origin of the high energy-conversion efficiency of F<sub>1</sub>-ATPase.Proc Natl Acad Sci U S A2019
31506355Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins.Proc Natl Acad Sci U S A2019
31219783Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'.Elife2019
29442996Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies.Elife2018
30082384Structure of the <i>EmrE</i> multidrug transporter and its use for inhibitor peptide design.Proc Natl Acad Sci U S A2018
29998846Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size.Elife2018
30152054Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides.Protein Sci2018
28709262Coexisting origins of subdiffusion in internal dynamics of proteins.Phys Rev E2017
29083306Exploratory search during directed navigation in <i>C. elegans</i> and <i>Drosophila</i> larva.Elife2017
29111975Kinesin motility is driven by subdomain dynamics.Elife2017
27135391A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes.J Phys Chem B2016
24484045Enhanced chemical synthesis at soft interfaces: a universal reaction-adsorption mechanism in microcompartments.Phys Rev Lett2014
25453082Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism.Proc Natl Acad Sci U S A2014
25066036Development of multiscale models for complex chemical systems: from H+Hâ¿¿ to biomolecules (Nobel Lecture).Angew Chem Int Ed Engl2014
24811667Investigations of α-helix⿿β-sheet transition pathways in a miniprotein using the finite-temperature string method.J Chem Phys2014
24669953First passage analysis of the folding of a β-sheet miniprotein: is it more realistic than the standard equilibrium approach?J Phys Chem B2014
23268557A simplified confinement method for calculating absolute free energies and free energy and entropy differences.J Phys Chem B2013
24043807A gating mechanism of pentameric ligand-gated ion channels.Proc Natl Acad Sci U S A2013
24224786Hemoglobin Bohr effects: atomic origin of the histidine residue contributions.Biochemistry2013
23621790New 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.J Phys Chem B2013
22409258Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin.J Phys Chem B2012
22696415Asymmetric synthesis of pochoninâ¿¿E and F, revision of their proposed structure, and their conversion to potent Hsp90 inhibitors.Chemistry2012
22511791Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1.J Biol Chem2012
22219368Strandwise translocation of a DNA glycosylase on undamaged DNA.Proc Natl Acad Sci U S A2012
21415366Unsuspected pathway of the allosteric transition in hemoglobin.Proc Natl Acad Sci U S A2011
22098742A conformational transition in the myosin VI converter contributes to the variable step size.Biophys J2011
21806105Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method.J Chem Phys2011
21619043Determining the conformational change that accompanies donor-acceptor distance fluctuations: an umbrella sampling analysis.J Phys Chem B2011
21685880Behind the folding funnel diagram.Nat Chem Biol2011
21361558Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.J Chem Phys2011
19889642Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM.J Biol Chem2010
20133745PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis.Proc Natl Acad Sci U S A2010
20152155The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis.Structure2010
20151415Dynamical aspects of molecular recognition.J Mol Recognit2010
20399183Pi release from myosin: a simulation analysis of possible pathways.Structure2010
20424124Role of conformation transitions in adenylate kinase.Proc Natl Acad Sci U S A2010
20435910Protein dynamics investigated by inherent structure analysis.Proc Natl Acad Sci U S A2010
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Collaborators

Christopher M Dobson
University of Cambridge
Co-authored papers 22
James Andrew McCammon
Co-authored papers 17
Gregory A Petsko
Helen and Robert Appel Alzheimer's Disease Research Institute, Cornell University
Co-authored papers 15
Aaron R Dinner
James Franck Institute, Institute for Biophysical Dynamics, University of Chicago
Co-authored papers 14
Michele Vendruscolo
University of Cambridge
Co-authored papers 11
John Kuriyan
University of California berkeley
Co-authored papers 11
Andrej Sali (CM4AI)
University of California San Francisco
Co-authored papers 9
Angela M Gronenborn
University of Pittsburgh
Co-authored papers 9
Yaoqi Zhou
Co-authored papers 8
Diane Joseph-McCarthy
Boston University
Co-authored papers 8
Robert Bruccoleri
Co-authored papers 7
Herman W T van Vlijmen
Leiden Academic Centre for Drug Research (LACDR), Leiden University
Co-authored papers 6
Charles L Brooks
University of Michigan ann arbor
Co-authored papers 5
David A Case
Rutgers University
Co-authored papers 4
Stephen W Michnick
Co-authored papers 4
Subramanyam Swaminathan
Brookhaven National Laboratory
Co-authored papers 4
David J States
OncProTech LLC
Co-authored papers 4
Eugene I Shakhnovich
Harvard University
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Memorial Sloan-Kettering Cancer Center
Co-authored papers 4
Stuart L Schreiber
Broad Institute
Co-authored papers 3
Michael Nilges
Institut Pasteur
Co-authored papers 3
Ron Elber
Institute for Computational Engineering and Science, University of Texas at Austin
Co-authored papers 3
John-Marc Chandonia
Lawrence Berkeley National Laboratory
Co-authored papers 3
Roland L Dunbrack
Fox Chase Cancer Center
Co-authored papers 3
Shoshana J Wodak
VIB-VUB Center for Structural Biology
Co-authored papers 2
Adam P Willard
Massachusetts Institute of Technology
Co-authored papers 2
Lorna J Smith
University of Oxford
Co-authored papers 2
Dino Moras
Laboratory IGBMC (Institute of Genetics and of Molecular and Cellular Biology)
Co-authored papers 2
Richard L Stevens
School of Biomedical Sciences and Pharmacy, University of Newcastle
Co-authored papers 2
Ryoji Matsumoto
Atopy Research Center, Juntendo University Graduate School of Medicine
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Release 1.2