Gordon Crippen - Related publications

Affiliations: 
University of Michigan, Ann Arbor, Ann Arbor, MI 
Area:
Pharmaceutical Chemistry, Molecular Biology, Biochemistry
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Michael E, Simonson T. How much can physics do for protein design? Current Opinion in Structural Biology. 72: 46-54. PMID 34461593 DOI: 10.1016/j.sbi.2021.07.011   
2021 Zweckstetter M. NMR hawk-eyed view of AlphaFold2 structures. Protein Science : a Publication of the Protein Society. PMID 34469019 DOI: 10.1002/pro.4175   
2021 Kondra S, Chen F, Chen Y, Chen Y, Collette CJ, Xu W. A study of a hierarchical structure of proteins and ligand binding sites of receptors using the TSR-based structure comparison method and development of a size-filtering feature designed for comparing different sizes of protein structures. Proteins. PMID 34392570 DOI: 10.1002/prot.26215   
2021 Miao Z, Wang Q, Xiao X, Kamal GM, Song L, Zhang X, Li C, Zhou X, Jiang B, Liu M. CSI-LSTM: a web server to predict protein secondary structure using bidirectional long short term memory and NMR chemical shifts. Journal of Biomolecular Nmr. PMID 34510297 DOI: 10.1007/s10858-021-00383-9   
2021 Caldararu O, Ekberg V, Logan DT, Oksanen E, Ryde U. Exploring ligand dynamics in protein crystal structures with ensemble refinement. Acta Crystallographica. Section D, Structural Biology. 77: 1099-1115. PMID 34342282 DOI: 10.1107/S2059798321006513   
2021 Schwarz D, Georges G, Kelm S, Shi J, Vangone A, Deane CM. Co-evolutionary Distance Predictions Contain Flexibility Information. Bioinformatics (Oxford, England). PMID 34383892 DOI: 10.1093/bioinformatics/btab562   
2021 Liang S, Li Z, Zhan J, Zhou Y. De Novo protein design by an energy function based on series expansion in distance and orientation dependence. Bioinformatics (Oxford, England). PMID 34406339 DOI: 10.1093/bioinformatics/btab598   
2021 Seong K, Krasileva K. Computational structural genomics unravels common folds and novel families in the secretome of fungal phytopathogen . Molecular Plant-Microbe Interactions : Mpmi. PMID 34415195 DOI: 10.1094/MPMI-03-21-0071-R   
2021 Florio G, Pugno NM, Buehler MJ, Puglisi G. A coarse-grained mechanical model for folding and unfolding of tropoelastin with possible mutations. Acta Biomaterialia. PMID 34303013 DOI: 10.1016/j.actbio.2021.07.032   
2021 Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. International Journal of Molecular Sciences. 22. PMID 34502559 DOI: 10.3390/ijms22179653   
2021 Verburgt J, Kihara D. Benchmarking of structure refinement methods for protein complex models. Proteins. PMID 34309909 DOI: 10.1002/prot.26188   
2021 Park T, Woo H, Yang J, Kwon S, Won J, Seok C. Protein Oligomer Structure Prediction using GALAXY in CASP14. Proteins. PMID 34363243 DOI: 10.1002/prot.26203   
2021 Jedhe GS, Arora PS. Hydrogen bond surrogate helices as minimal mimics of protein α-helices. Methods in Enzymology. 656: 1-25. PMID 34325784 DOI: 10.1016/bs.mie.2021.04.007   
2021 Nakamura T, Yokaichiya T, Fedorov DG. Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems. The Journal of Physical Chemistry Letters. 8757-8762. PMID 34478310 DOI: 10.1021/acs.jpclett.1c02510   
2021 Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK. Energy penalties enhance flexible receptor docking in a model cavity. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34475217 DOI: 10.1073/pnas.2106195118   
2021 Ye X, Mayne L, Englander SW. A conserved strategy for structure change and energy transduction in Hsp104 and other AAA+ protein motors. The Journal of Biological Chemistry. 101066. PMID 34384781 DOI: 10.1016/j.jbc.2021.101066   
2021 Santhouse JR, Rao SR, Horne WS. Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics. Methods in Enzymology. 656: 93-122. PMID 34325801 DOI: 10.1016/bs.mie.2021.04.009   
2021 Cao Y, Das P, Chenthamarakshan V, Chen PY, Melnyk I, Shen Y. Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. Proceedings of Machine Learning Research. 139: 1261-1271. PMID 34423306   
2021 Zhao J, Liu M, Zang J, Yang S, Chen R, Zhao X, Ding L. Molecular docking, 3D-QASR and molecular dynamics simulations of thiazoles Pin1 inhibitors. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 34499020 DOI: 10.1080/07391102.2021.1975568   
2021 Kryshtafovych A, Moult J, Billings WM, Della Corte D, Fidelis K, Kwon S, Olechnovič K, Seok C, Venclovas Č, Won J. Modeling SARS-CoV2 proteins in the CASP-commons experiment. Proteins. PMID 34462960 DOI: 10.1002/prot.26231   
2021 Bai B, Zou R, Chan HCS, Li H, Yuan S. MolADI: A Web Server for Automatic Analysis of Protein-Small Molecule Dynamic Interactions. Molecules (Basel, Switzerland). 26. PMID 34361778 DOI: 10.3390/molecules26154625   
2021 Quadir F, Roy RS, Soltanikazemi E, Cheng J. DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling. Frontiers in Molecular Biosciences. 8: 716973. PMID 34497831 DOI: 10.3389/fmolb.2021.716973   
2021 Aggarwal R, Gupta A, Chelur V, Jawahar CV, Priyakumar UD. DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks. Journal of Chemical Information and Modeling. PMID 34374539 DOI: 10.1021/acs.jcim.1c00799   
2021 Mishra S, Looger LL, Porter LL. A sequence-based method for predicting extant fold switchers that undergo α-helix ↔ β-strand transitions. Biopolymers. e23471. PMID 34498740 DOI: 10.1002/bip.23471   
2021 Mortuza SM, Zheng W, Zhang C, Li Y, Pearce R, Zhang Y. Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nature Communications. 12: 5011. PMID 34408149 DOI: 10.1038/s41467-021-25316-w   
2021 Fowler NJ, Sljoka A, Williamson MP. The accuracy of NMR protein structures in the Protein Data Bank. Structure (London, England : 1993). PMID 34331857 DOI: 10.1016/j.str.2021.07.001   
2021 Gupta A, Vijayan V, Pant P, Kaur P, Singh TP, Sharma P, Sharma S. Structure prediction and discovery of inhibitors against phosphopantothenoyl cysteine synthetase of . Journal of Biomolecular Structure & Dynamics. 1-13. PMID 34348086 DOI: 10.1080/07391102.2021.1958699   
2021 Egbert M, Ghani U, Ashizawa R, Kotelnikov S, Nguyen T, Desta I, Hashemi N, Padhorny D, Kozakov D, Vajda S. Assessing the binding properties of CASP14 targets and models. Proteins. PMID 34368994 DOI: 10.1002/prot.26209   
2021 Cucuzza S, Güntert P, Plückthun A, Zerbe O. An automated iterative approach for protein structure refinement using pseudocontact shifts. Journal of Biomolecular Nmr. PMID 34338940 DOI: 10.1007/s10858-021-00376-8   
2021 Sharma B, Dill KA. MELD-accelerated molecular dynamics help determine amyloid fibril structures. Communications Biology. 4: 942. PMID 34354239 DOI: 10.1038/s42003-021-02461-y   
2021 T RR, Saharay M, Smith JC, Krishnan M. Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding. The Journal of Physical Chemistry. B. PMID 34423989 DOI: 10.1021/acs.jpcb.1c01227   
2021 Gervasoni S, Spencer J, Hinchliffe P, Pedretti A, Vairoletti F, Mahler G, Mulholland AJ. A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors. Proteins. PMID 34455628 DOI: 10.1002/prot.26227   
2021 Zhang Y, Li A. High-throughput virtual screening and microsecond MD simulations to identify potential sugar mimic of the solute-binding protein BlAXBP of the ABC transporter from Bifidobacterium animalis subsp. Lactis. Computational Biology and Chemistry. 93: 107541. PMID 34273720 DOI: 10.1016/j.compbiolchem.2021.107541   
2021 Parkman JA, Barksdale CA, Michaelis DJ. CAN: A new program to streamline preparation of molecular coordinate files for molecular dynamics simulations. Journal of Computational Chemistry. PMID 34411332 DOI: 10.1002/jcc.26729   
2021 Dass R, Corlianò E, Mulder FAA. The contribution of electrostatics to hydrogen exchange in the unfolded protein state. Biophysical Journal. PMID 34370996 DOI: 10.1016/j.bpj.2021.08.003   
2021 Malliavin TE. Tandem domain structure determination based on a systematic enumeration of conformations. Scientific Reports. 11: 16925. PMID 34413388 DOI: 10.1038/s41598-021-96370-z   
2021 Lv TM, Chen DL, Liang JJ, Bai M, Lin B, Huang XX, Ma GX, Song SJ. Structural Revisions of Two Highly Aromatic Naphthoquinone-Derived Dimers Based on NMR Analysis, Computer-Assisted Structure Elucidation Methods, and Computations. Organic Letters. PMID 34436914 DOI: 10.1021/acs.orglett.1c02626   
2021 Shmool TA, Martin LK, Bui-Le L, Moya-Ramirez I, Kotidis P, Matthews RP, Venter GA, Kontoravdi C, Polizzi KM, Hallett JP. An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid. Chemical Science. 12: 9528-9545. PMID 34349928 DOI: 10.1039/d1sc02520a   
2021 Tosstorff A, Cole JC, Bartelt R, Kuhn B. Augmenting structure-based design with experimental protein-ligand interaction data: molecular recognition, interactive visualization and rescoring. Chemmedchem. PMID 34342128 DOI: 10.1002/cmdc.202100387   
2021 Boucher L, Somani S, Negron C, Ma W, Jacobs S, Chan W, Malia T, Obmolova G, Teplyakov A, Gilliland GL, Luo J. Surface Salt bridges Contribute to the Extreme Thermal Stability of an FN3-like domain from a thermophilic bacterium. Proteins. PMID 34405904 DOI: 10.1002/prot.26218   
2021 Murata H, Imakawa H, Koga N, Chikenji G. The register shift rules for βαβ-motifs for de novo protein design. Plos One. 16: e0256895. PMID 34460870 DOI: 10.1371/journal.pone.0256895   
2021 Motono C, Yanagida S, Sato M, Hirokawa T. MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts. Bioinformatics (Oxford, England). PMID 34289011 DOI: 10.1093/bioinformatics/btab538   
2021 Dreydoppel M, Dorn B, Modig K, Akke M, Weininger U. Transition-State Compressibility and Activation Volume of Transient Protein Conformational Fluctuations. Jacs Au. 1: 833-842. PMID 34467336 DOI: 10.1021/jacsau.1c00062   
2021 Koukos PI, Réau M, Bonvin AMJJ. Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. Journal of Chemical Information and Modeling. PMID 34436890 DOI: 10.1021/acs.jcim.1c00796   
2021 Barozet A, Molloy K, Vaisset M, Zanon C, Fauret P, Siméon T, Cortés J. MoMA-LoopSampler: A web server to exhaustively sample protein loop conformations. Bioinformatics (Oxford, England). PMID 34432000 DOI: 10.1093/bioinformatics/btab584   
2021 Liu YC, Yang DY, Sheu SY. Insights into the free energy landscape and salt-controlled mechanism of the conformational conversions between human telomeric G-quadruplex structures. International Journal of Biological Macromolecules. PMID 34536474 DOI: 10.1016/j.ijbiomac.2021.09.057   
2021 Dubrow A, Kim I, Topo E, Cho JH. Understanding the Binding Transition State After the Conformational Selection Step: The Second Half of the Molecular Recognition Process Between NS1 of the 1918 Influenza Virus and Host p85β. Frontiers in Molecular Biosciences. 8: 716477. PMID 34307465 DOI: 10.3389/fmolb.2021.716477   
2021 Dubrow A, Kim I, Topo E, Cho JH. Understanding the Binding Transition State After the Conformational Selection Step: The Second Half of the Molecular Recognition Process Between NS1 of the 1918 Influenza Virus and Host p85β. Frontiers in Molecular Biosciences. 8: 716477. PMID 34307465 DOI: 10.3389/fmolb.2021.716477   
2021 Voith von Voithenberg L, Barth A, Trauschke V, Demarco B, Tyagi S, Koehler C, Lemke EA, Lamb DC. Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34389669 DOI: 10.1073/pnas.2025578118   
2021 Padhi AK, Kumar A, Haruna KI, Sato H, Tamura H, Nagatoishi S, Tsumoto K, Yamaguchi A, Iraha F, Takahashi M, Sakamoto K, Zhang KYJ. An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes. Briefings in Bioinformatics. PMID 34415295 DOI: 10.1093/bib/bbab338