Parag Kumar Mallick - Related publications

Affiliations: 
2002 University of California, Los Angeles, Los Angeles, CA 
NOTE: We are testing a new system for identifying relevant work based on semantic analysis that identifies similarities between recently published papers and the current author's publications. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches.
50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 Verburgt J, Kihara D. Benchmarking of structure refinement methods for protein complex models. Proteins. PMID 34309909 DOI: 10.1002/prot.26188   
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 Tunyasuvunakool K, Adler J, Wu Z, Green T, Zielinski M, Žídek A, Bridgland A, Cowie A, Meyer C, Laydon A, Velankar S, Kleywegt GJ, Bateman A, Evans R, Pritzel A, et al. Highly accurate protein structure prediction for the human proteome. Nature. PMID 34293799 DOI: 10.1038/s41586-021-03828-1   
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 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 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 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 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 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 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 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 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 Ruff KM, Pappu RV. AlphaFold and implications for intrinsically disordered proteins. Journal of Molecular Biology. 167208. PMID 34418423 DOI: 10.1016/j.jmb.2021.167208   
2021 Ye L, Wu P, Peng Z, Gao J, Liu J, Yang J. Improved estimation of model quality using predicted inter-residue distance. Bioinformatics (Oxford, England). PMID 34473228 DOI: 10.1093/bioinformatics/btab632   
2021 Halder P, Mitra P. Human prion protein: exploring the thermodynamic stability and structural dynamics of its pathogenic mutants. Journal of Biomolecular Structure & Dynamics. 1-17. PMID 34338141 DOI: 10.1080/07391102.2021.1957715   
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 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 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 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 Singh M, Becker M, Godwin ARF, Baldock C. Structural studies of elastic fibre and microfibrillar proteins. Matrix Biology Plus. 12: 100078. PMID 34355160 DOI: 10.1016/j.mbplus.2021.100078   
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 Breunig SL, Tirrell DA. Incorporation of proline analogs into recombinant proteins expressed in Escherichia coli. Methods in Enzymology. 656: 545-571. PMID 34325798 DOI: 10.1016/bs.mie.2021.05.008   
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 Kono F, Tamada T. Neutron crystallography for the elucidation of enzyme catalysis. Current Opinion in Structural Biology. 71: 36-42. PMID 34214927 DOI: 10.1016/j.sbi.2021.05.007   
2021 Kono F, Tamada T. Neutron crystallography for the elucidation of enzyme catalysis. Current Opinion in Structural Biology. 71: 36-42. PMID 34214927 DOI: 10.1016/j.sbi.2021.05.007   
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 Sauer DB, Wang B, Sudar JC, Song J, Marden J, Rice WJ, Wang DN. The ups and downs of elevator-type di-/tricarboxylate membrane transporters. The Febs Journal. PMID 34403567 DOI: 10.1111/febs.16158   
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 Zheng W, Li Y, Zhang C, Zhou X, Pearce R, Bell EW, Huang X, Zhang Y. Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14. Proteins. PMID 34331351 DOI: 10.1002/prot.26193   
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 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 Ultsch M, Holliday MJ, Gerhardy S, Moran P, Scales SJ, Gupta N, Oltrabella F, Chiu C, Fairbrother W, Eigenbrot C, Kirchhofer D. Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif. Communications Biology. 4: 916. PMID 34316015 DOI: 10.1038/s42003-021-02387-5   
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 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 Tan KP, Singh K, Hazra A, Madhusudhan MS. Peptide bond planarity constrains hydrogen bond geometry and influences secondary structure conformations. Current Research in Structural Biology. 3: 1-8. PMID 34382009 DOI: 10.1016/j.crstbi.2020.11.002   
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 Herman MA, Aiello BR, DeLong JD, Garcia-Ruiz H, González AL, Hwang W, McBeth C, Stojković EA, Trakselis MA, Yakoby N. A Unifying Framework for Understanding Biological Structures and Functions Across Levels of Biological Organization. Integrative and Comparative Biology. PMID 34302339 DOI: 10.1093/icb/icab167   
2021 Poghosyan AH, Shahinyan AA, Kirakosyan GR, Ayvazyan NM, Mamasakhlisov YS, Papoian GA. A molecular dynamics study of protein denaturation induced by sulfonate-based surfactants. Journal of Molecular Modeling. 27: 261. PMID 34432183 DOI: 10.1007/s00894-021-04882-2   
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 Song KC, Molina AV, Chen R, Gagnon IA, Koh YH, Roux B, Sosnick TR. Folding and misfolding of potassium channel monomers during assembly and tetramerization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34413192 DOI: 10.1073/pnas.2103674118   
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 Xu G, Wang Q, Ma J. OPUS-X: An Open-Source Toolkit for Protein Torsion Angles, Secondary Structure, Solvent Accessibility, Contact Map Predictions, and 3D Folding. Bioinformatics (Oxford, England). PMID 34478500 DOI: 10.1093/bioinformatics/btab633   
2021 Dongre AV, Das S, Bellur A, Kumar S, Chandrashekarmath A, Karmakar T, Balaram P, Balasubramanian S, Balaram H. Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation. Biophysical Journal. PMID 34302792 DOI: 10.1016/j.bpj.2021.07.014   
2021 Dongre AV, Das S, Bellur A, Kumar S, Chandrashekarmath A, Karmakar T, Balaram P, Balasubramanian S, Balaram H. Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation. Biophysical Journal. PMID 34302792 DOI: 10.1016/j.bpj.2021.07.014   
2021 Ortega-Alarcon D, Claveria-Gimeno R, Vega S, Jorge-Torres OC, Esteller M, Abian O, Velazquez-Campoy A. Stabilization Effect of Intrinsically Disordered Regions on Multidomain Proteins: The Case of the Methyl-CpG Protein 2, MeCP2. Biomolecules. 11. PMID 34439881 DOI: 10.3390/biom11081216   
2021 Sun B, Lv J, Chen J, Liu Z, Zhou Y, Liu L, Jin Y, Wang F. Size-Selective VAILase Proteolysis Provides Dynamic Insights into Protein Structures. Analytical Chemistry. PMID 34291915 DOI: 10.1021/acs.analchem.1c02042   
2021 Sun B, Lv J, Chen J, Liu Z, Zhou Y, Liu L, Jin Y, Wang F. Size-Selective VAILase Proteolysis Provides Dynamic Insights into Protein Structures. Analytical Chemistry. PMID 34291915 DOI: 10.1021/acs.analchem.1c02042