Martin Karplus - Related publications

Harvard University, Cambridge, MA, United States 
electronic structure, geometry, and dynamics of molecules of chemical and biological interest
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Smith RD, Carlson HA. Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. Journal of Chemical Information and Modeling. PMID 33599485 DOI: 10.1021/acs.jcim.0c01002   
2021 Jin Y, Johannissen LO, Hay S. Predicting New Protein Conformations from Molecular Dynamics Simulation Conformational Landscapes and Machine Learning. Proteins. PMID 33629765 DOI: 10.1002/prot.26068   
2021 Roche R, Bhattacharya S, Bhattacharya D. Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins. Plos Computational Biology. 17: e1008753. PMID 33621244 DOI: 10.1371/journal.pcbi.1008753   
2021 Sikkema HR, Poolman B. In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy. Scientific Reports. 11: 5756. PMID 33707507 DOI: 10.1038/s41598-021-85003-0   
2021 Di Rienzo L, Miotto M, Bò L, Ruocco G, Raimondo D, Milanetti E. Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network. Frontiers in Molecular Biosciences. 8: 626837. PMID 33718433 DOI: 10.3389/fmolb.2021.626837   
2021 Hays JM, Boland E, Kasson PM. Inference of Joint Conformational Distributions from Separately Acquired Experimental Measurements. The Journal of Physical Chemistry Letters. 12: 1606-1611. PMID 33596657 DOI: 10.1021/acs.jpclett.0c03623   
2021 Diaz DB, Appavoo SD, Bogdanchikova AF, Lebedev Y, McTiernan TJ, Dos Passos Gomes G, Yudin AK. Illuminating the dark conformational space of macrocycles using dominant rotors. Nature Chemistry. PMID 33589789 DOI: 10.1038/s41557-020-00620-y   
2021 Norn C, Wicky BIM, Juergens D, Liu S, Kim D, Tischer D, Koepnick B, Anishchenko I, , Baker D, Ovchinnikov S. Protein sequence design by conformational landscape optimization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33712545 DOI: 10.1073/pnas.2017228118   
2021 Ravikumar A, de Brevern AG, Srinivasan N. Conformational Strain Indicated by Ramachandran Angles for the Protein Backbone Is Only Weakly Related to the Flexibility. The Journal of Physical Chemistry. B. PMID 33666418 DOI: 10.1021/acs.jpcb.1c00168   
2021 Nath P, Goyal A. Structure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans. Journal of Molecular Modeling. 27: 106. PMID 33694107 DOI: 10.1007/s00894-021-04721-4   
2021 Zou J, Xiao S, Simmerling C, Raleigh DP. Quantitative Analysis of Protein Unfolded State Energetics: Experimental and Computational Studies Demonstrate That Non-Native Side-Chain Interactions Stabilize Local Native Backbone Structure. The Journal of Physical Chemistry. B. PMID 33779182 DOI: 10.1021/acs.jpcb.0c08922   
2021 Fernandes DD, Neale C, Gomes GW, Li Y, Malik A, Pandey A, Orazietti AP, Wang X, Ye L, Scott Prosser R, Gradinaru CC. Ligand modulation of the conformational dynamics of the A adenosine receptor revealed by single-molecule fluorescence. Scientific Reports. 11: 5910. PMID 33723285 DOI: 10.1038/s41598-021-84069-0   
2021 Fernandes DD, Neale C, Gomes GW, Li Y, Malik A, Pandey A, Orazietti AP, Wang X, Ye L, Scott Prosser R, Gradinaru CC. Ligand modulation of the conformational dynamics of the A adenosine receptor revealed by single-molecule fluorescence. Scientific Reports. 11: 5910. PMID 33723285 DOI: 10.1038/s41598-021-84069-0   
2021 Gianni S, Freiberger MI, Jemth P, Ferreiro DU, Wolynes PG, Fuxreiter M. Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly. Accounts of Chemical Research. PMID 33550810 DOI: 10.1021/acs.accounts.0c00813   
2021 Hsu DJ, Leshchev D, Kosheleva I, Kohlstedt KL, Chen LX. Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations. The Journal of Chemical Physics. 154: 105101. PMID 33722011 DOI: 10.1063/5.0039194   
2021 Dandekar BR, Ahalawat N, Mondal J. Reconciling Conformational Heterogeneity and Substrate Recognition in Cytochrome P450. Biophysical Journal. PMID 33675756 DOI: 10.1016/j.bpj.2021.02.040   
2021 Zhuravlev PI, Hinczewski M, Thirumalai D. Low Force Unfolding of a Single-Domain Protein by Parallel Pathways. The Journal of Physical Chemistry. B. PMID 33565314 DOI: 10.1021/acs.jpcb.0c11308   
2021 Sanders JC, Holmstrom ED. Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins. Essays in Biochemistry. PMID 33600559 DOI: 10.1042/EBC20200022   
2021 He X, Huang N, Qiu Y, Zhang J, Liu Y, Yin XL, Lu S. Conformational Selection Mechanism Provides Structural Insights into the Optimization of APC-Asef Inhibitors. Molecules (Basel, Switzerland). 26. PMID 33670371 DOI: 10.3390/molecules26040962   
2021 Namsani S, Pramanik D, Khan MA, Roy S, Singh JK. Metadynamics-based enhanced sampling protocol for virtual screening: case study for 3CLpro protein for SARS-CoV-2. Journal of Biomolecular Structure & Dynamics. 1-16. PMID 33663346 DOI: 10.1080/07391102.2021.1892530   
2021 Dawson WM, Lang EJM, Rhys GG, Shelley KL, Williams C, Brady RL, Crump MP, Mulholland AJ, Woolfson DN. Structural resolution of switchable states of a de novo peptide assembly. Nature Communications. 12: 1530. PMID 33750792 DOI: 10.1038/s41467-021-21851-8   
2021 Zhuang Y, Bureau HR, Lopez C, Bucher R, Quirk S, Hernandez R. Energetics and structure of alanine-rich α-helices via Adaptive Steered Molecular Dynamics (ASMD). Biophysical Journal. PMID 33775636 DOI: 10.1016/j.bpj.2021.03.017   
2021 Hernandes IS, Da Silva HC, Dos Santos HF, De Almeida WB. Unveiling the Molecular Structure of Antimalarial Drugs Chloroquine and Hydroxychloroquine in Solution through Analysis of H NMR Chemical Shifts. The Journal of Physical Chemistry. B. PMID 33760611 DOI: 10.1021/acs.jpcb.1c00609   
2021 Gopi S, Lukose B, Naganathan AN. Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains. The Journal of Physical Chemistry. B. PMID 33818099 DOI: 10.1021/acs.jpcb.1c00972   
2021 King E, Qi R, Li H, Luo R, Aitchison E. Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations. Journal of Chemical Theory and Computation. PMID 33764050 DOI: 10.1021/acs.jctc.0c01305   
2021 Krishnan VV, Bentley T, Xiong A, Maitra K. Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs. International Journal of Molecular Sciences. 22. PMID 33573010 DOI: 10.3390/ijms22031364   
2021 Dias D'Andréa É, Sebastian Retel J, Diehl A, Schmieder P, Oschkinat H, Ricardo Pires J. NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi. Journal of Structural Biology. 107715. PMID 33705979 DOI: 10.1016/j.jsb.2021.107715   
2021 Buchholz I, McDonnell T, Nestler P, Tharad S, Kulke M, Radziszewska A, Ripoll VM, Schmidt F, Hammer E, Toca-Herrera JL, Rahman A, Delcea M. Specific domain V reduction of beta-2-glycoprotein I induces protein flexibility and alters pathogenic antibody binding. Scientific Reports. 11: 4542. PMID 33633190 DOI: 10.1038/s41598-021-84021-2   
2021 Feng X, Li F, Ding M, Zhang R, Shi T, Jiang W. Molecular dynamic simulation: Structural insights of multi-stranded curdlan in aqueous solution. Carbohydrate Polymers. 261: 117844. PMID 33766340 DOI: 10.1016/j.carbpol.2021.117844   
2021 Ludwig J, Smith J, Pfaendtner J. Analyzing the Long Time-Scale Dynamics of Uremic Toxins Bound to Sudlow Site II in Human Serum Albumin. The Journal of Physical Chemistry. B. PMID 33715376 DOI: 10.1021/acs.jpcb.1c00221   
2021 Estrada Pabón JD, Haddox HK, Van Aken G, Pendleton IM, Eramian H, Singer JM, Schrier J. The Role of Configurational Entropy in Miniprotein Stability. The Journal of Physical Chemistry. B. PMID 33739115 DOI: 10.1021/acs.jpcb.0c09888   
2021 Hiranuma N, Park H, Baek M, Anishchenko I, Dauparas J, Baker D. Improved protein structure refinement guided by deep learning based accuracy estimation. Nature Communications. 12: 1340. PMID 33637700 DOI: 10.1038/s41467-021-21511-x   
2021 Pinto SMV, Tasinato N, Barone V, Zanetti-Polzi L, Daidone I. A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures. The Journal of Chemical Physics. 154: 084105. PMID 33639764 DOI: 10.1063/5.0038913   
2021 Wang B, Su Z, Wu Y. Computational Assessment of Protein-Protein Binding Affinity by Reverse Engineering the Energetics in Protein Complexes. Genomics, Proteomics & Bioinformatics. PMID 33838354 DOI: 10.1016/j.gpb.2021.03.004   
2021 Caldararu O, Blundell TL, Kepp KP. A base measure of precision for protein stability predictors: structural sensitivity. Bmc Bioinformatics. 22: 88. PMID 33632133 DOI: 10.1186/s12859-021-04030-w   
2021 Jaskolski M, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Rupp B, Wlodawer A. Crystallographic models of SARS-CoV-2 3CL: in-depth assessment of structure quality and validation. Iucrj. 8: 238-256. PMID 33708401 DOI: 10.1107/S2052252521001159   
2021 Khamari L, Pramanik U, Shekhar S, Mohanakumar S, Mukherjee S. Thermal Reversibility and Structural Stability in Lysozyme Induced by Epirubicin Hydrochloride. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 33703900 DOI: 10.1021/acs.langmuir.1c00179   
2021 Sagar A, Jeffries CM, Petoukhov MV, Svergun DI, Bernadó P. Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method. Journal of Chemical Theory and Computation. PMID 33725442 DOI: 10.1021/acs.jctc.1c00014   
2021 Crean RM, Biler M, van der Kamp MW, Hengge AC, Kamerlin SCL. Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases. Journal of the American Chemical Society. PMID 33661624 DOI: 10.1021/jacs.0c11806   
2021 Kim J, Mandal R, Hilty C. 2D NMR spectroscopy of refolding RNase Sa using polarization transfer from hyperpolarized water. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 326: 106942. PMID 33713971 DOI: 10.1016/j.jmr.2021.106942   
2021 Freiberger MI, Wolynes PG, Ferreiro DU, Fuxreiter M. Frustration in Fuzzy Protein Complexes Leads to Interaction Versatility. The Journal of Physical Chemistry. B. 125: 2513-2520. PMID 33667107 DOI: 10.1021/acs.jpcb.0c11068   
2021 Mondal B, Nagesh J, Reddy G. Double Domain Swapping in Human γC and γD Crystallin Drives Early Stages of Aggregation. The Journal of Physical Chemistry. B. PMID 33566611 DOI: 10.1021/acs.jpcb.0c07833   
2021 Miller EB, Murphy RB, Sindhikara D, Borrelli KW, Grisewood MJ, Ranalli F, Dixon SL, Jerome S, Boyles NA, Day T, Ghanakota P, Mondal S, Rafi SB, Troast DM, Abel R, et al. Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding. Journal of Chemical Theory and Computation. PMID 33779166 DOI: 10.1021/acs.jctc.1c00136   
2021 Turan HT, Meuwly M. Spectroscopy, Dynamics, and Hydration of -Nitrosylated Myoglobin. The Journal of Physical Chemistry. B. PMID 33724027 DOI: 10.1021/acs.jpcb.0c10353   
2021 Turan HT, Meuwly M. Spectroscopy, Dynamics, and Hydration of -Nitrosylated Myoglobin. The Journal of Physical Chemistry. B. PMID 33724027 DOI: 10.1021/acs.jpcb.0c10353   
2021 Barge S, Jade D, Gosavi G, Talukdar NC, Borah J. In-silico screening for identification of potential inhibitors against SARS-CoV-2 transmembrane serine protease 2 (TMPRSS2). European Journal of Pharmaceutical Sciences : Official Journal of the European Federation For Pharmaceutical Sciences. 162: 105820. PMID 33775827 DOI: 10.1016/j.ejps.2021.105820   
2021 Ching WY, Adhikari P, Jawad B, Podgornik R. Ultra-large-scale quantum chemical computation of bio-molecular systems: the case of Spike protein of SARS-CoV-2 virus. Computational and Structural Biotechnology Journal. PMID 33623641 DOI: 10.1016/j.csbj.2021.02.004   
2021 Jhaveri A, Maisuria D, Varga M, Mohammadyani D, Johnson ME. Thermodynamics and Free Energy Landscape of BAR-Domain Dimerization from Molecular Simulations. The Journal of Physical Chemistry. B. PMID 33826319 DOI: 10.1021/acs.jpcb.0c10992   
2021 Ajadi MB, Soremekun OS, Elrashedy AA, Olotu FA, Kumalo HM, Soliman MES. Probing Protein-Protein Interactions and Druggable Site Identification: Mechanistic Binding Events between Ubiquitin and Zinc Finger with UFM1-Specific Peptidase Domain Protein (ZUFSP). Combinatorial Chemistry & High Throughput Screening. PMID 33538664 DOI: 10.2174/1386207324666210203175142   
2021 Zhang S, Gong W, Han Z, Liu Y, Li C. Insight into Shared Properties and Differential Dynamics and Specificity of Secretory Phospholipase A Family Members. The Journal of Physical Chemistry. B. PMID 33780247 DOI: 10.1021/acs.jpcb.1c01315