Klaus Schulten - Related publications

University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
theoretical biophysics
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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 Mori T, Jung J, Kobayashi C, Dokainish HM, Re S, Sugita Y. Elucidation of Interactions Regulating Conformational Stability and Dynamics of SARS-CoV-2 S-Protein. Biophysical Journal. PMID 33484712 DOI: 10.1016/j.bpj.2021.01.012   
2021 Duran T, Minatovicz B, Bai J, Shin D, Mohammadiarani H, Chaudhuri B. Molecular Dynamics Simulation to Uncover the Mechanisms of Protein Instability During Freezing. Journal of Pharmaceutical Sciences. PMID 33421436 DOI: 10.1016/j.xphs.2021.01.002   
2021 Hervø-Hansen S, Højgaard C, Johansson KE, Wang Y, Wahni K, Young D, Messens J, Teilum K, Lindorff-Larsen K, Winther JR. Charge Interactions in a Highly Charge-Depleted Protein. Journal of the American Chemical Society. PMID 33529004 DOI: 10.1021/jacs.0c10789   
2021 Steinmetz A, Yvorra T, Retailleau P, Lantz O, Schmidt F. Datasets and analyses of molecular dynamics simulations of covalent binary and ternary complexes of MHC class I-related molecule/T-cell receptor (MR1/TCR) agonists to understand complex formation and conditions of fluorescent labelling. Data in Brief. 34: 106704. PMID 33506079 DOI: 10.1016/j.dib.2020.106704   
2021 Li Y, Bedi RK, Wiedmer L, Sun X, Huang D, Caflisch A. Atomistic and Thermodynamic Analysis of N6-Methyladenosine (mA) Recognition by the Reader Domain of YTHDC1. Journal of Chemical Theory and Computation. PMID 33472367 DOI: 10.1021/acs.jctc.0c01136   
2021 Milorey B, Schweitzer-Stenner R, Andrews B, Schwalbe H, Urbanc B. Short peptides as predictors for the structure of polyarginine sequences in disordered proteins. Biophysical Journal. PMID 33453267 DOI: 10.1016/j.bpj.2020.12.026   
2021 Kumar R, Saran S. Comparative modelling unravels the structural features of eukaryotic TCTP implicated in its multifunctional properties: an in silico approach. Journal of Molecular Modeling. 27: 20. PMID 33410974 DOI: 10.1007/s00894-020-04630-y   
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 Romero-Tamayo S, Laplaza R, Velazquez-Campoy A, Villanueva R, Medina M, Ferreira P. W196 and the -Hairpin Motif Modulate the Redox Switch of Conformation and the Biomolecular Interaction Network of the Apoptosis-Inducing Factor. Oxidative Medicine and Cellular Longevity. 2021: 6673661. PMID 33510840 DOI: 10.1155/2021/6673661   
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 Koulgi S, Jani V, Nair V, Saini JS, Phukan S, Sonavane U, Joshi R, Kamboj R, Palle V. Molecular dynamics of hERG channel: insights into understanding the binding of small molecules for detuning cardiotoxicity. Journal of Biomolecular Structure & Dynamics. 1-17. PMID 33494645 DOI: 10.1080/07391102.2021.1875883   
2021 Bhatia S, Krishnamoorthy G, Udgaonkar JB. Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein. Journal of the American Chemical Society. PMID 33430589 DOI: 10.1021/jacs.0c11097   
2021 Deng Z, Yuan B, Yang K. Cardiolipin Selectively Binds to the Interface of SemiSWEET and Regulates Its Dimerization. The Journal of Physical Chemistry Letters. 1940-1946. PMID 33591759 DOI: 10.1021/acs.jpclett.1c00022   
2021 Gupta D, Tiwari P, Haque MA, Sachdeva E, Hassan MI, Ethayathulla AS, Kaur P. Structural insights into the transient closed conformation and pH dependent ATPase activity of S.Typhi GyraseB N- terminal domain. Archives of Biochemistry and Biophysics. 108786. PMID 33548211 DOI: 10.1016/j.abb.2021.108786   
2021 Hou Q, Pucci F, Ancien F, Kwasigroch JM, Bourgeas R, Rooman M. SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs. Bioinformatics (Oxford, England). PMID 33471089 DOI: 10.1093/bioinformatics/btab034   
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 Tesei G, Martins JM, Kunze MBA, Wang Y, Crehuet R, Lindorff-Larsen K. DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles. Plos Computational Biology. 17: e1008551. PMID 33481784 DOI: 10.1371/journal.pcbi.1008551   
2021 Gopal SM, Wingbermühle S, Schnatwinkel J, Juber S, Herrmann C, Schäfer LV. Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields. The Journal of Physical Chemistry. B. 125: 24-35. PMID 33382616 DOI: 10.1021/acs.jpcb.0c08702   
2021 Mahmoudinobar F, Nilsson BL, Dias CL. Effects of Ions and Small Compounds on the Structure of Aβ Monomers. The Journal of Physical Chemistry. B. 125: 1085-1097. PMID 33481611 DOI: 10.1021/acs.jpcb.0c09617   
2021 Seifi B, Wallin S. The C-terminal domain of transcription factor RfaH: Folding, fold switching and energy landscape. Biopolymers. e23420. PMID 33521926 DOI: 10.1002/bip.23420   
2021 Paiz EA, Lewis KA, Whitten ST. Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins. Molecules (Basel, Switzerland). 26. PMID 33530506 DOI: 10.3390/molecules26030634   
2021 Di Luca A, Kaila VRI. Molecular strain in the active/deactive-transition modulates domain coupling in respiratory complex I. Biochimica Et Biophysica Acta. Bioenergetics. 148382. PMID 33513365 DOI: 10.1016/j.bbabio.2021.148382   
2021 He J, Han Z, Farooq QUA, Li C. Study on functional sites in human multidrug resistance protein 1 (hMRP1). Proteins. PMID 33469960 DOI: 10.1002/prot.26049   
2021 Thompson EJ, Paul A, Iavarone AT, Klinman JP. Identification of Thermal Conduits That Link the Protein-Water Interface to the Active Site Loop and Catalytic Base in Enolase. Journal of the American Chemical Society. PMID 33395523 DOI: 10.1021/jacs.0c09423   
2021 Bedford JT, Poutsma J, Diawara N, Greene LH. The nature of persistent interactions in two model β-grasp proteins reveals the advantage of symmetry in stability. Journal of Computational Chemistry. PMID 33534913 DOI: 10.1002/jcc.26477   
2021 Sellner M, Fischer A, Don CG, Smieško M. Conformational Landscape of Cytochrome P450 Reductase Interactions. International Journal of Molecular Sciences. 22. PMID 33498551 DOI: 10.3390/ijms22031023   
2021 Mei LC, Wang YL, Wu FX, Wang F, Hao GF, Yang GF. HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study. Briefings in Bioinformatics. PMID 33406224 DOI: 10.1093/bib/bbaa373   
2021 Shrestha R, Fajardo JE, Fiser A. Residue-based pharmacophore approaches to study protein-protein interactions. Current Opinion in Structural Biology. 67: 205-211. PMID 33486430 DOI: 10.1016/j.sbi.2020.12.016   
2021 Milanetti E, Miotto M, Di Rienzo L, Monti M, Gosti G, Ruocco G. 2D Zernike polynomial expansion: Finding the protein-protein binding regions. Computational and Structural Biotechnology Journal. 19: 29-36. PMID 33363707 DOI: 10.1016/j.csbj.2020.11.051   
2021 Privat C, Granadino-Roldán JM, Bonet J, Santos Tomas M, Perez JJ, Rubio-Martinez J. Fragment dissolved molecular dynamics: a systematic and efficient method to locate binding sites. Physical Chemistry Chemical Physics : Pccp. PMID 33491698 DOI: 10.1039/d0cp05471b   
2021 Raich L, Meier K, Günther J, Christ CD, Noé F, Olsson S. Discovery of a hidden transient state in all bromodomain families. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33468647 DOI: 10.1073/pnas.2017427118   
2021 Quesada Moreno MM, Pinacho P, Perez C, Sekutor M, Schreiner PR, Schnell M. Do docking sites persist upon fluorination? The diadamantyl ether-aromatics challenge for rotational spectroscopy and theory. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 33512017 DOI: 10.1002/chem.202100078   
2021 Dang TKL, Nguyen T, Habeck M, Gültas M, Waack S. A graph-based algorithm for detecting rigid domains in protein structures. Bmc Bioinformatics. 22: 66. PMID 33579190 DOI: 10.1186/s12859-021-03966-3   
2021 Zhu M, Song LT, Liu RR, Zhai HL, Meng YJ, Ren CL. Selective inhibition mechanism of nitroxoline to the BET family: Insight from molecular simulations. Life Sciences. 119141. PMID 33529672 DOI: 10.1016/j.lfs.2021.119141   
2021 Ramanathan A, Ma H, Parvatikar A, Chennubhotla SC. Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins. Current Opinion in Structural Biology. 66: 216-224. PMID 33421906 DOI: 10.1016/j.sbi.2020.12.001   
2021 Mohd-Kipli F, Claridge JK, Habjanič J, Jiang A, Schnell JR. Conformational triggers associated with influenza matrix protein 1 polymerization. The Journal of Biological Chemistry. 100316. PMID 33516724 DOI: 10.1016/j.jbc.2021.100316   
2021 Labra-Núñez A, Cofas-Vargas LF, Gutiérrez-Magdaleno G, Gómez-Velasco H, Rodríguez-Hernández A, Rodríguez-Romero A, García-Hernández E. Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Archives of Biochemistry and Biophysics. 699: 108750. PMID 33421379 DOI: 10.1016/j.abb.2020.108750   
2021 Labra-Núñez A, Cofas-Vargas LF, Gutiérrez-Magdaleno G, Gómez-Velasco H, Rodríguez-Hernández A, Rodríguez-Romero A, García-Hernández E. Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Archives of Biochemistry and Biophysics. 699: 108750. PMID 33421379 DOI: 10.1016/j.abb.2020.108750   
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 Pfab J, Phan NM, Si D. DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33361332 DOI: 10.1073/pnas.2017525118   
2021 Gupta M, Venkatramani R, Ainavarapu SRK. Role of Ligand Binding Site in Modulating the Mechanical Stability of Proteins with β-Grasp Fold. The Journal of Physical Chemistry. B. PMID 33492970 DOI: 10.1021/acs.jpcb.0c08085   
2021 Crilly CJ, Brom JA, Kowalewski ME, Piszkiewicz S, Pielak GJ. Dried Protein Structure Revealed at the Residue Level by Liquid-Observed Vapor Exchange NMR. Biochemistry. PMID 33400518 DOI: 10.1021/acs.biochem.0c00863   
2021 Iacobucci GJ, Wen H, Helou M, Liu B, Zheng W, Popescu GK. Cross-subunit interactions that stabilize open states mediate gating in NMDA receptors. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33384330 DOI: 10.1073/pnas.2007511118   
2021 Vugmeyster L. Recent developments in deuterium solid-state NMR for the detection of slow motions in proteins. Solid State Nuclear Magnetic Resonance. 111: 101710. PMID 33450712 DOI: 10.1016/j.ssnmr.2020.101710   
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 Shah S, Chaple D, Arora S, Yende S, Mehta C, Nayak U. Prospecting for to treat COVID-19 via molecular docking models of the SARS-CoV-2. Journal of Biomolecular Structure & Dynamics. 1-9. PMID 33446077 DOI: 10.1080/07391102.2021.1872419   
2021 Dalal V, Dhankhar P, Singh V, Singh V, Rakhaminov G, Golemi-Kotra D, Kumar P. Structure-Based Identification of Potential Drugs Against FmtA of Staphylococcus aureus: Virtual Screening, Molecular Dynamics, MM-GBSA, and QM/MM. The Protein Journal. PMID 33421024 DOI: 10.1007/s10930-020-09953-6   
2021 Kabra A, Li Y. Conformational Dynamics of Deubiquitinase A and Functional Implications. Biochemistry. PMID 33417762 DOI: 10.1021/acs.biochem.0c00834   
2021 Walls B, Mazilkin AA, Mukhamedov BO, Ionov A, Smirnova IA, Ponomareva AV, Fleischer K, Kozlovskaya NA, Shulyatev DA, Abrikosov IA, Shvets IV, Bozhko SI. Nanodomain structure of single crystalline nickel oxide. Scientific Reports. 11: 3496. PMID 33568704 DOI: 10.1038/s41598-021-82070-1