{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,22]],"date-time":"2025-03-22T10:52:40Z","timestamp":1742640760320,"version":"3.37.3"},"reference-count":159,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,3,21]],"date-time":"2019-03-21T00:00:00Z","timestamp":1553126400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100010242","name":"Jiangsu Planned Projects for Postdoctoral Research Funds","doi-asserted-by":"publisher","award":["1601168C"],"id":[{"id":"10.13039\/501100010242","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Jiangsu College Natural Science Research Key Program","award":["17KJA520004"]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2016M590495"],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31872723"],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,21]]},"abstract":"Abstract<\/jats:title>Proteins are dynamical entities that undergo a plethora of conformational changes, accomplishing their biological functions. Molecular dynamics simulation and normal mode analysis methods have become the gold standard for studying protein dynamics, analyzing molecular mechanism and allosteric regulation of biological systems. The enormous amount of the ensemble-based experimental and computational data on protein structure and dynamics has presented a major challenge for the high-throughput modeling of protein regulation and molecular mechanisms. In parallel, bioinformatics and systems biology approaches including genomic analysis, coevolution and network-based modeling have provided an array of powerful tools that complemented and enriched biophysical insights by enabling high-throughput analysis of biological data and dissection of global molecular signatures underlying mechanisms of protein function and interactions in the cellular environment. These developments have provided a powerful interdisciplinary framework for quantifying the relationships between protein dynamics and allosteric regulation, allowing for high-throughput modeling and engineering of molecular mechanisms. Here, we review fundamental advances in protein dynamics, network theory and coevolutionary analysis that have provided foundation for rapidly growing computational tools for modeling of allosteric regulation. We discuss recent developments in these interdisciplinary areas bridging computational biophysics and network biology, focusing on promising applications in allosteric regulations, including the investigation of allosteric communication pathways, protein\u2013DNA\/RNA interactions and disease mutations in genomic medicine. We conclude by formulating and discussing future directions and potential challenges facing quantitative computational investigations of allosteric regulatory mechanisms in protein systems.<\/jats:p>","DOI":"10.1093\/bib\/bbz029","type":"journal-article","created":{"date-parts":[[2019,2,23]],"date-time":"2019-02-23T12:08:35Z","timestamp":1550923715000},"page":"815-835","source":"Crossref","is-referenced-by-count":65,"title":["Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications"],"prefix":"10.1093","volume":"21","author":[{"given":"Zhongjie","family":"Liang","sequence":"first","affiliation":[{"name":"School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China"}]},{"given":"Gennady M","family":"Verkhivker","sequence":"first","affiliation":[{"name":"Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, USA"},{"name":"Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, USA"}]},{"given":"Guang","family":"Hu","sequence":"first","affiliation":[{"name":"School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China"}]}],"member":"286","published-online":{"date-parts":[[2019,3,21]]},"reference":[{"key":"2020051819280779800_ref1","doi-asserted-by":"crossref","first-page":"6503","DOI":"10.1021\/acs.chemrev.5b00590","article-title":"Protein allostery and conformational dynamics","volume":"116","author":"Guo","year":"2016","journal-title":"Chem Rev"},{"key":"2020051819280779800_ref2","doi-asserted-by":"crossref","first-page":"1500","DOI":"10.1093\/molbev\/mst065","article-title":"Protein conformational diversity correlates with evolutionary rate","volume":"30","author":"Javier Zea","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2020051819280779800_ref3","doi-asserted-by":"crossref","first-page":"5051","DOI":"10.1039\/C3CS60474H","article-title":"A theoretical view of protein dynamics","volume":"43","author":"Orozco","year":"2014","journal-title":"Chem Soc Rev"},{"key":"2020051819280779800_ref4","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1021\/cr040426m","article-title":"Molecular dynamics: survey of methods for simulating the activity of proteins","volume":"106","author":"Adcock","year":"2006","journal-title":"Chem Rev"},{"key":"2020051819280779800_ref5","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1146\/annurev.biophys.093008.131258","article-title":"Global dynamics of proteins: bridging between structure and function","volume":"39","author":"Bahar","year":"2010","journal-title":"Annu Rev Biophys"},{"key":"2020051819280779800_ref6","first-page":"659","article-title":"Structural database resources for biological macromolecules","volume":"18","author":"Abriata","year":"2017","journal-title":"Brief Bioinform"},{"key":"2020051819280779800_ref7","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1016\/j.drudis.2017.01.005","article-title":"The application of principal component analysis to drug discovery and biomedical data","volume":"22","author":"Giuliani","year":"2017","journal-title":"Drug Discov Today"},{"key":"2020051819280779800_ref8","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1002\/wcms.1142","article-title":"High-throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure","volume":"3","author":"Hospital","year":"2013","journal-title":"Wiley Interdiscip Rev Comput Mol Sci"},{"key":"2020051819280779800_ref9","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1093\/bioinformatics\/btu769","article-title":"Achievements and challenges in structural bioinformatics and computational biophysics","volume":"31","author":"Samish","year":"2015","journal-title":"Bioinformatics"},{"key":"2020051819280779800_ref10","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.plrev.2017.11.003","article-title":"Network science of biological systems at different scales: a review","volume":"24","author":"Gosak","year":"2018","journal-title":"Phys Life Rev"},{"key":"2020051819280779800_ref11","doi-asserted-by":"crossref","first-page":"2776","DOI":"10.1016\/j.febslet.2007.05.021","article-title":"Network analysis of protein dynamics","volume":"581","author":"B\u00f6de","year":"2007","journal-title":"FEBS Lett"},{"key":"2020051819280779800_ref12","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.sbi.2006.01.002","article-title":"Network and graph analyses of folding free energy surfaces","volume":"16","author":"Caflisch","year":"2006","journal-title":"Curr Opin Struct Biol"},{"key":"2020051819280779800_ref13","doi-asserted-by":"crossref","first-page":"6057","DOI":"10.1021\/jp0761665","article-title":"Coarse master equations for peptide folding dynamics","volume":"112","author":"Buchete","year":"2008","journal-title":"J Phys Chem B"},{"key":"2020051819280779800_ref14","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.jmgm.2013.10.003","article-title":"Network visualization of conformational sampling during molecular dynamics simulation","volume":"46","author":"Ahlstrom","year":"2013","journal-title":"J Mol Graph Model"},{"key":"2020051819280779800_ref15","doi-asserted-by":"crossref","first-page":"72323","DOI":"10.1063\/1.5027580","article-title":"Conformational analysis of replica exchange MD: temperature-dependent Markov networks for FF amyloid peptides","volume":"149","author":"Narayan","year":"2018","journal-title":"J Chem Phys"},{"key":"2020051819280779800_ref16","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bib\/bbv070","article-title":"MST2-RASSF protein\u2013protein interactions through SARAH domains","volume":"17","author":"S\u00e1nchez-Sanz","year":"2016","journal-title":"Brief Bioinform"},{"key":"2020051819280779800_ref17","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005051","article-title":"SARAH domain-mediated MST2-RASSF dimeric interactions","volume":"12","author":"S\u00e1nchez-Sanz","year":"2016","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref18","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1016\/j.sbi.2015.02.005","article-title":"Conformational diversity and the emergence of sequence signatures during evolution","volume":"32","author":"Parisi","year":"2015","journal-title":"Curr Opin Struct Biol"},{"key":"2020051819280779800_ref19","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1038\/nbt.3769","article-title":"Mutation effects predicted from sequence co-variation","volume":"35","author":"Hopf","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2020051819280779800_ref20","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.sbi.2017.10.014","article-title":"Inter-residue, inter-protein and inter-family coevolution: bridging the scales","volume":"50","author":"Szurmant","year":"2018","journal-title":"Curr Opin Struct Biol"},{"key":"2020051819280779800_ref21","doi-asserted-by":"crossref","first-page":"13567","DOI":"10.1073\/pnas.1508584112","article-title":"From residue coevolution to protein conformational ensembles and functional dynamics","volume":"112","author":"Sutto","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2020051819280779800_ref22","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1021\/acs.jpcb.7b07529","article-title":"Characterizing conformational dynamics of proteins using evolutionary couplings","volume":"122","author":"Feng","year":"2018","journal-title":"J Phys Chem B"},{"key":"2020051819280779800_ref23","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.str.2015.10.025","article-title":"Residues coevolution guides the systematic identification of alternative functional conformations in proteins","volume":"24","author":"Sfriso","year":"2016","journal-title":"Structure"},{"key":"2020051819280779800_ref24","doi-asserted-by":"crossref","first-page":"e1000544","DOI":"10.1371\/journal.pcbi.1000544","article-title":"Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein","volume":"5","author":"Atilgan","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref25","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1016\/j.bpj.2010.05.020","article-title":"Manipulation of conformational change in proteins by single-residue perturbations","volume":"99","author":"Atilgan","year":"2010","journal-title":"Biophys J"},{"key":"2020051819280779800_ref26","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1073\/pnas.0601602103","article-title":"Modularity and community structure in networks","volume":"103","author":"Newman","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2020051819280779800_ref27","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/j.pharmthera.2013.01.016","article-title":"Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review","volume":"138","author":"Csermely","year":"2013","journal-title":"Pharmacol Ther"},{"key":"2020051819280779800_ref28","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrg1272","article-title":"Network biology: understanding the cell's functional organization","volume":"5","author":"Barab\u00e1si","year":"2004","journal-title":"Nat Rev Genet"},{"key":"2020051819280779800_ref29","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1093\/bfgp\/els039","article-title":"Protein structure networks","volume":"11","author":"Greene","year":"2012","journal-title":"Brief Funct Genomics"},{"key":"2020051819280779800_ref30","doi-asserted-by":"crossref","first-page":"2202","DOI":"10.1093\/bioinformatics\/bts352","article-title":"ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality","volume":"28","author":"Szalay-Beko","year":"2012","journal-title":"Bioinformatics"},{"key":"2020051819280779800_ref31","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1006\/jmbi.1999.3058","article-title":"Identification of side-chain clusters in protein structures by a graph spectral method","volume":"292","author":"Kannan","year":"1999","journal-title":"J Mol Biol"},{"key":"2020051819280779800_ref32","doi-asserted-by":"crossref","first-page":"1419","DOI":"10.1007\/s00726-014-1710-6","article-title":"The construction of an amino acid network for understanding protein structure and function","volume":"46","author":"Yan","year":"2014","journal-title":"Amino Acids"},{"key":"2020051819280779800_ref33","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.csbj.2016.06.002","article-title":"Biophysical and computational methods to analyze amino acid interaction networks in proteins","volume":"14","author":"O'Rourke","year":"2016","journal-title":"Comput Struct Biotechnol J"},{"key":"2020051819280779800_ref34","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1002\/wcms.1186","article-title":"Computing protein dynamics from protein structure with elastic network models","volume":"4","author":"Bastolla","year":"2014","journal-title":"Wiley Interdiscip Rev Comput Mol Sci"},{"key":"2020051819280779800_ref35","doi-asserted-by":"crossref","first-page":"28","DOI":"10.3389\/fmolb.2015.00028","article-title":"Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity","volume":"2","author":"Papaleo","year":"2015","journal-title":"Front Mol Biosci"},{"key":"2020051819280779800_ref36","doi-asserted-by":"crossref","first-page":"6620","DOI":"10.1073\/pnas.0810961106","article-title":"Dynamical networks in tRNA:protein complexes","volume":"106","author":"Sethi","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2020051819280779800_ref37","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.gene.2008.06.002","article-title":"Evolutionary conservation of protein vibrational dynamics","volume":"422","author":"Maguid","year":"2008","journal-title":"Gene"},{"key":"2020051819280779800_ref38","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1093\/bioinformatics\/btv103","article-title":"Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution","volume":"31","author":"Mao","year":"2015","journal-title":"Bioinformatics"},{"key":"2020051819280779800_ref39","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/nrg3414","article-title":"Emerging methods in protein co-evolution","volume":"14","author":"Juan","year":"2013","journal-title":"Nat Rev Genet"},{"key":"2020051819280779800_ref40","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000931","article-title":"Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs","volume":"6","author":"Liu","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref41","doi-asserted-by":"crossref","first-page":"2049","DOI":"10.1021\/acs.jpcb.6b11976","article-title":"Evolutionary covariance combined with molecular dynamics predicts a framework for allostery in the MutS DNA mismatch repair protein","volume":"121","author":"Lakhani","year":"2017","journal-title":"J Phys Chem B"},{"key":"2020051819280779800_ref42","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1021\/cr3002356","article-title":"Protein contact networks: an emerging paradigm in chemistry","volume":"113","author":"Di Paola","year":"2013","journal-title":"Chem Rev"},{"key":"2020051819280779800_ref43","doi-asserted-by":"crossref","first-page":"e117","DOI":"10.1371\/journal.pcbi.0030117","article-title":"Ligand binding and circular permutation modify residue interaction network in DHFR","volume":"3","author":"Hu","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref44","doi-asserted-by":"crossref","first-page":"248","DOI":"10.3389\/fphar.2015.00248","article-title":"Molecular features of interaction between VEGFA and anti-angiogenic drugs used in retinal diseases: a computational approach","volume":"6","author":"Platania","year":"2015","journal-title":"Front Pharmacol"},{"key":"2020051819280779800_ref45","doi-asserted-by":"crossref","first-page":"2768","DOI":"10.1093\/bioinformatics\/btx349","article-title":"MD-TASK: a software suite for analyzing molecular dynamics trajectories","volume":"33","author":"Brown","year":"2017","journal-title":"Bioinformatics"},{"key":"2020051819280779800_ref46","doi-asserted-by":"crossref","first-page":"W375","DOI":"10.1093\/nar\/gkw383","article-title":"NAPS: network analysis of protein structures","volume":"44","author":"Chakrabarty","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2020051819280779800_ref47","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.tibs.2011.01.002","article-title":"Analyzing and visualizing residue networks of protein structures","volume":"36","author":"Doncheva","year":"2011","journal-title":"Trends Biochem Sci"},{"key":"2020051819280779800_ref48","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"key":"2020051819280779800_ref49","doi-asserted-by":"crossref","first-page":"W367","DOI":"10.1093\/nar\/gkw315","article-title":"The RING 2.0 web server for high quality residue interaction networks","volume":"44","author":"Piovesan","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2020051819280779800_ref50","doi-asserted-by":"crossref","first-page":"e5998","DOI":"10.7717\/peerj.5998","article-title":"RIP-MD: a tool to study residue interaction networks in protein molecular dynamics","volume":"6","author":"Contreras-Riquelme","year":"2018","journal-title":"PeerJ"},{"key":"2020051819280779800_ref51","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1471-2105-4-2","article-title":"An automated method for finding molecular complexes in large protein interaction networks","volume":"4","author":"Bader","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2020051819280779800_ref52","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1186\/1471-2105-12-436","article-title":"clusterMaker: a multi-algorithm clustering plugin for Cytoscape","volume":"12","author":"Morris","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2020051819280779800_ref53","doi-asserted-by":"crossref","first-page":"4159","DOI":"10.1529\/biophysj.105.064485","article-title":"A network representation of protein structures: implications for protein stability","volume":"89","author":"Brinda","year":"2005","journal-title":"Biophys J"},{"key":"2020051819280779800_ref54","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1042\/BJ20050434","article-title":"Insights into the quaternary association of proteins through structure graphs: a case study of lectins","volume":"391","author":"Brinda","year":"2005","journal-title":"Biochem J"},{"key":"2020051819280779800_ref55","doi-asserted-by":"crossref","first-page":"146","DOI":"10.2174\/138920309787847590","article-title":"Intra and inter-molecular communications through protein structure network","volume":"10","author":"Vishveshwara","year":"2009","journal-title":"Curr Protein Pept Sci"},{"key":"2020051819280779800_ref56","doi-asserted-by":"crossref","first-page":"15711","DOI":"10.1073\/pnas.0704459104","article-title":"A study of communication pathways in methionyl-tRNA synthetase by molecular dynamics simulations and structure network analysis","volume":"104","author":"Ghosh","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2020051819280779800_ref57","doi-asserted-by":"crossref","first-page":"53","DOI":"10.2174\/1875036201105010053","article-title":"GraProStr\u2014graphs of protein structures: a tool for constructing the graphs and generating graph parameters for protein structures","volume":"5","author":"Vijayabaskar","year":"2011","journal-title":"Open Bioinforma J"},{"key":"2020051819280779800_ref58","doi-asserted-by":"crossref","first-page":"1399","DOI":"10.1002\/pro.2333","article-title":"An automated approach to network features of protein structure ensembles","volume":"22","author":"Bhattacharyya","year":"2013","journal-title":"Protein Sci"},{"key":"2020051819280779800_ref59","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1002\/jcc.21688","article-title":"Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces","volume":"32","author":"Seeber","year":"2011","journal-title":"J Comput Chem"},{"key":"2020051819280779800_ref60","doi-asserted-by":"crossref","first-page":"3704","DOI":"10.1016\/j.bpj.2010.08.079","article-title":"Interaction energy based protein structure networks","volume":"99","author":"Vijayabaskar","year":"2010","journal-title":"Biophys J"},{"key":"2020051819280779800_ref61","doi-asserted-by":"crossref","first-page":"W554","DOI":"10.1093\/nar\/gky381","article-title":"gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations","volume":"46","author":"Ser\u00e7inoglu","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2020051819280779800_ref62","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1021\/ci400639r","article-title":"PyInteraph: a framework for the analysis of interaction networks in structural ensembles of proteins","volume":"54","author":"Tiberti","year":"2014","journal-title":"J Chem Inf Model"},{"key":"2020051819280779800_ref63","doi-asserted-by":"crossref","first-page":"2838","DOI":"10.1038\/s41598-017-01498-6","article-title":"An optimal distance cutoff for contact-based protein structure networks using side-chain centers of mass","volume":"7","author":"Salamanca Viloria","year":"2017","journal-title":"Sci Rep"},{"key":"2020051819280779800_ref64","doi-asserted-by":"crossref","first-page":"7821","DOI":"10.1073\/pnas.122653799","article-title":"Community structure in social and biological networks","volume":"99","author":"Girvan","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2020051819280779800_ref65","doi-asserted-by":"crossref","first-page":"E1428","DOI":"10.1073\/pnas.1120536109","article-title":"Allosteric pathways in imidazole glycerol phosphate synthase","volume":"109","author":"Rivalta","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2020051819280779800_ref66","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/glycob\/cwt095","article-title":"Structural glycobiology of heparin dynamics on the exosite 2 of coagulation cascade proteases: implications for glycosaminoglycans antithrombotic activity","volume":"24","author":"Pol-Fachin","year":"2014","journal-title":"Glycobiology"},{"key":"2020051819280779800_ref67","doi-asserted-by":"crossref","first-page":"2579","DOI":"10.1016\/j.bbagen.2018.08.007","article-title":"Dynamics of DDB2-DDB1 complex under different naturally-occurring mutants in xeroderma pigmentosum disease","volume":"1862","author":"Feltes","year":"2018","journal-title":"Biochim Biophys Acta Gen Subj"},{"key":"2020051819280779800_ref68","doi-asserted-by":"crossref","first-page":"2949","DOI":"10.1021\/ct300377a","article-title":"Exploring residue component contributions to dynamical network models of allostery","volume":"8","author":"Van Wart","year":"2012","journal-title":"J Chem Theory Comput"},{"key":"2020051819280779800_ref69","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1021\/ct4008603","article-title":"Weighted implementation of suboptimal paths (WISP): an optimized algorithm and tool for dynamical network analysis","volume":"10","author":"Van Wart","year":"2014","journal-title":"J Chem Theory Comput"},{"key":"2020051819280779800_ref70","doi-asserted-by":"crossref","first-page":"3000","DOI":"10.1093\/bioinformatics\/bts546","article-title":"NetworkView: 3D display and analysis of protein\u00b7RNA interaction networks","volume":"28","author":"Eargle","year":"2012","journal-title":"Bioinformatics"},{"key":"2020051819280779800_ref71","doi-asserted-by":"crossref","first-page":"1865","DOI":"10.1021\/ci300213c","article-title":"xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures","volume":"52","author":"Pasi","year":"2012","journal-title":"J Chem Inf Model"},{"key":"2020051819280779800_ref72","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1021\/ci200289s","article-title":"JGromacs: a Java package for analyzing protein simulations","volume":"52","author":"M\u00fcnz","year":"2012","journal-title":"J Chem Inf Model"},{"key":"2020051819280779800_ref73","doi-asserted-by":"crossref","first-page":"e1005711","DOI":"10.1371\/journal.pcbi.1005711","article-title":"Polymodal allosteric regulation of type 1 serine\/threonine kinase receptors via a conserved electrostatic lock","volume":"13","author":"Botello-Smith","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref74","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1039\/C4FD00024B","article-title":"Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs","volume":"169","author":"Allain","year":"2014","journal-title":"Faraday Discuss"},{"issue":"Suppl 2","key":"2020051819280779800_ref75","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s12859-015-0855-y","article-title":"Dissecting protein architecture with communication blocks and communicating segment pairs","volume":"17","author":"Karami","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"2020051819280779800_ref76","doi-asserted-by":"crossref","first-page":"16126","DOI":"10.1038\/s41598-018-34508-2","article-title":"\"Infostery\" analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations","volume":"8","author":"Karami","year":"2018","journal-title":"Sci Rep"},{"key":"2020051819280779800_ref77","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.1021\/ct400977r","article-title":"Determination of signaling pathways in proteins through network theory: importance of the topology","volume":"10","author":"Ribeiro","year":"2014","journal-title":"J Chem Theory Comput"},{"key":"2020051819280779800_ref78","doi-asserted-by":"crossref","first-page":"1835","DOI":"10.1021\/jp509906m","article-title":"Energy propagation and network energetic coupling in proteins","volume":"119","author":"Ribeiro","year":"2015","journal-title":"J Phys Chem B"},{"key":"2020051819280779800_ref79","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1016\/j.bpj.2015.06.013","article-title":"MDN: a web portal for network analysis of molecular dynamics simulations","volume":"109","author":"Ribeiro","year":"2015","journal-title":"Biophys J"},{"key":"2020051819280779800_ref80","doi-asserted-by":"crossref","first-page":"2180","DOI":"10.1002\/prot.24574","article-title":"Detecting protein atom correlations using correlation of probability of recurrence","volume":"82","author":"Fataftah","year":"2014","journal-title":"Proteins"},{"key":"2020051819280779800_ref81","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1186\/s12859-015-0621-1","article-title":"Weighted protein residue networks based on joint recurrences between residues","volume":"16","author":"Karain","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"2020051819280779800_ref82","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1002\/prot.25261","article-title":"The adaptive nature of protein residue networks","volume":"85","author":"Karain","year":"2017","journal-title":"Proteins"},{"key":"2020051819280779800_ref83","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1007\/s12551-017-0330-2","article-title":"Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank","volume":"9","author":"Wako","year":"2017","journal-title":"Biophys Rev"},{"key":"2020051819280779800_ref84","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/S0006-3495(04)74086-2","article-title":"Small-world communication of residues and significance for protein dynamics","volume":"86","author":"Atilgan","year":"2004","journal-title":"Biophys J"},{"key":"2020051819280779800_ref85","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1093\/bib\/bbm014","article-title":"High-throughput modeling and analysis of protein structural dynamics","volume":"8","author":"Liu","year":"2007","journal-title":"Brief Bioinform"},{"key":"2020051819280779800_ref86","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1089\/cmb.2017.0171","article-title":"The relationship between low-frequency motions and community structure of residue network in protein molecules","volume":"25","author":"Sun","year":"2018","journal-title":"J Comput Biol"},{"key":"2020051819280779800_ref87","doi-asserted-by":"crossref","first-page":"2504","DOI":"10.1021\/ct400096f","article-title":"A mixed protein structure network and elastic network model approach to predict the structural communication in biomolecular systems: the PDZ2 domain from tyrosine phosphatase 1E as a case study","volume":"9","author":"Raimondi","year":"2013","journal-title":"J Chem Theory Comput"},{"key":"2020051819280779800_ref88","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1093\/bioinformatics\/btu718","article-title":"WebPSN: a web server for high-throughput investigation of structural communication in biomacromolecules","volume":"31","author":"Seeber","year":"2015","journal-title":"Bioinformatics"},{"key":"2020051819280779800_ref89","doi-asserted-by":"crossref","first-page":"2483264","DOI":"10.1155\/2017\/2483264","article-title":"Comparative study of elastic network model and protein contact network for protein complexes: the hemoglobin case","volume":"2017","author":"Hu","year":"2017","journal-title":"Biomed Res Int"},{"key":"2020051819280779800_ref90","doi-asserted-by":"crossref","first-page":"2235","DOI":"10.1039\/C7MB00355B","article-title":"Network-based modelling and percolation analysis of conformational dynamics and activation in the CDK2 and CDK4 proteins: dynamic and energetic polarization of the kinase lobes may determine divergence of the regulatory mechanisms","volume":"13","author":"Verkhivker","year":"2017","journal-title":"Mol Biosyst"},{"key":"2020051819280779800_ref91","doi-asserted-by":"crossref","first-page":"e86547","DOI":"10.1371\/journal.pone.0086547","article-title":"Allosteric regulation of the Hsp90 dynamics and stability by client recruiter cochaperones: protein structure network modeling","volume":"9","author":"Blacklock","year":"2014","journal-title":"PLoS One"},{"key":"2020051819280779800_ref92","doi-asserted-by":"crossref","first-page":"78102","DOI":"10.1103\/PhysRevLett.94.078102","article-title":"Protein structural change upon ligand binding: linear response theory","volume":"94","author":"Ikeguchi","year":"2005","journal-title":"Phys Rev Lett"},{"key":"2020051819280779800_ref93","doi-asserted-by":"crossref","first-page":"e1002154","DOI":"10.1371\/journal.pcbi.1002154","article-title":"Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning","volume":"7","author":"Gerek","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref94","doi-asserted-by":"crossref","first-page":"1692","DOI":"10.1016\/j.str.2015.07.002","article-title":"Cooperative dynamics of intact AMPA and NMDA glutamate receptors: similarities and subfamily-specific differences","volume":"23","author":"Dutta","year":"2015","journal-title":"Structure"},{"key":"2020051819280779800_ref95","doi-asserted-by":"crossref","first-page":"W374","DOI":"10.1093\/nar\/gkx385","article-title":"DynOmics: dynamics of structural proteome and beyond","volume":"45","author":"Li","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2020051819280779800_ref96","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1021\/acs.jcim.6b00775","article-title":"Perturbation-response scanning reveals key residues for allosteric control in Hsp70","volume":"57","author":"Penkler","year":"2017","journal-title":"J Chem Inf Model"},{"key":"2020051819280779800_ref97","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.bbagen.2018.10.009","article-title":"Biophysical simulations and structure-based modeling of residue interaction networks in the tumor suppressor proteins reveal functional role of cancer mutation hotspots in molecular communication","volume":"1863","author":"Verkhivker","year":"2019","journal-title":"Biochim Biophys Acta Gen Subj"},{"key":"2020051819280779800_ref98","doi-asserted-by":"crossref","first-page":"6899","DOI":"10.1038\/s41598-018-25329-4","article-title":"Dissecting structure-encoded determinants of allosteric cross-talk between post-translational modification sites in the Hsp90 chaperones","volume":"8","author":"Stetz","year":"2018","journal-title":"Sci Rep"},{"key":"2020051819280779800_ref99","doi-asserted-by":"crossref","first-page":"e169586","DOI":"10.1371\/journal.pone.0169586","article-title":"A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations","volume":"12","author":"Michetti","year":"2017","journal-title":"PLoS One"},{"key":"2020051819280779800_ref100","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nsb881","article-title":"Evolutionarily conserved networks of residues mediate allosteric communication in proteins","volume":"10","author":"S\u00fcel","year":"2003","journal-title":"Nat Struct Biol"},{"key":"2020051819280779800_ref101","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1002\/pro.2258","article-title":"Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface","volume":"22","author":"Nichols","year":"2013","journal-title":"Protein Sci"},{"key":"2020051819280779800_ref102","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1016\/j.cell.2009.07.038","article-title":"Protein sectors: evolutionary units of three-dimensional structure","volume":"138","author":"Halabi","year":"2009","journal-title":"Cell"},{"key":"2020051819280779800_ref103","doi-asserted-by":"crossref","first-page":"W8","DOI":"10.1093\/nar\/gkt427","article-title":"MISTIC: mutual information server to infer coevolution","volume":"41","author":"Simonetti","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2020051819280779800_ref104","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0130203","article-title":"Molecular determinants underlying binding specificities of the ABL kinase inhibitors: combining alanine scanning of binding hot spots with network analysis of residue interactions and coevolution","volume":"10","author":"Tse","year":"2015","journal-title":"PLoS One"},{"key":"2020051819280779800_ref105","doi-asserted-by":"crossref","first-page":"e1005299","DOI":"10.1371\/journal.pcbi.1005299","article-title":"Computational analysis of residue interaction networks and coevolutionary relationships in the Hsp70 chaperones: a community-hopping model of allosteric regulation and communication","volume":"13","author":"Stetz","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref106","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1093\/molbev\/msv178","article-title":"Using THz spectroscopy, evolutionary network analysis methods, and MD simulation to map the evolution of allosteric communication pathways in c-type lysozymes","volume":"33","author":"Woods","year":"2016","journal-title":"Mol Biol Evol"},{"key":"2020051819280779800_ref107","doi-asserted-by":"crossref","first-page":"37290","DOI":"10.1038\/srep37290","article-title":"Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors","volume":"6","author":"Woods","year":"2016","journal-title":"Sci Rep"},{"key":"2020051819280779800_ref108","doi-asserted-by":"crossref","first-page":"6370","DOI":"10.1021\/acs.chemrev.5b00631","article-title":"Emerging computational methods for the rational discovery of allosteric drugs","volume":"116","author":"Wagner","year":"2016","journal-title":"Chem Rev"},{"key":"2020051819280779800_ref109","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.sbi.2016.06.017","article-title":"Computational approaches to investigating allostery","volume":"41","author":"Schueler-Furman","year":"2016","journal-title":"Curr Opin Struct Biol"},{"key":"2020051819280779800_ref110","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.cell.2013.03.034","article-title":"Allostery in disease and in drug discovery","volume":"153","author":"Nussinov","year":"2013","journal-title":"Cell"},{"key":"2020051819280779800_ref111","doi-asserted-by":"crossref","first-page":"1042","DOI":"10.1016\/j.str.2009.06.008","article-title":"The origin of allosteric functional modulation: multiple pre-existing pathways","volume":"17","author":"del Sol","year":"2009","journal-title":"Structure"},{"key":"2020051819280779800_ref112","doi-asserted-by":"crossref","first-page":"6463","DOI":"10.1021\/acs.chemrev.5b00544","article-title":"Controlling allosteric networks in proteins","volume":"116","author":"Dokholyan","year":"2016","journal-title":"Chem Rev"},{"key":"2020051819280779800_ref113","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.sbi.2015.03.001","article-title":"Protein contact network topology: a natural language for allostery","volume":"31","author":"Di Paola","year":"2015","journal-title":"Curr Opin Struct Biol"},{"key":"2020051819280779800_ref114","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.sbi.2014.02.004","article-title":"Computational approaches to mapping allosteric pathways","volume":"25","author":"Feher","year":"2014","journal-title":"Curr Opin Struct Biol"},{"key":"2020051819280779800_ref115","doi-asserted-by":"crossref","first-page":"1652","DOI":"10.1016\/j.bbamem.2016.01.010","article-title":"Computational approaches to detect allosteric pathways in transmembrane molecular machines","volume":"1858","author":"Stolzenberg","year":"2016","journal-title":"Biochim Biophys Acta"},{"key":"2020051819280779800_ref116","doi-asserted-by":"crossref","first-page":"43807","DOI":"10.1038\/srep43807","article-title":"Structure\u2013activity relationship in TLR4 mutations: atomistic molecular dynamics simulations and residue interaction network analysis","volume":"7","author":"Anwar","year":"2017","journal-title":"Sci Rep"},{"key":"2020051819280779800_ref117","doi-asserted-by":"crossref","first-page":"2876","DOI":"10.1038\/s41598-017-03003-5","article-title":"Network analysis reveals the recognition mechanism for dimer formation of bulb-type lectins","volume":"7","author":"Zhao","year":"2017","journal-title":"Sci Rep"},{"key":"2020051819280779800_ref118","doi-asserted-by":"crossref","first-page":"19940","DOI":"10.1038\/srep19940","article-title":"Allosteric pathways in the PPAR\u03b3-RXR\u03b1 nuclear receptor complex","volume":"6","author":"Ricci","year":"2016","journal-title":"Sci Rep"},{"key":"2020051819280779800_ref119","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1016\/j.bpj.2014.06.015","article-title":"Differences in allosteric communication pipelines in the inactive and active states of a GPCR","volume":"107","author":"Bhattacharya","year":"2014","journal-title":"Biophys J"},{"key":"2020051819280779800_ref120","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.str.2014.11.009","article-title":"Two pathways mediate interdomain allosteric regulation in pin1","volume":"23","author":"Guo","year":"2015","journal-title":"Structure"},{"key":"2020051819280779800_ref121","doi-asserted-by":"crossref","first-page":"e1003679","DOI":"10.1371\/journal.pcbi.1003679","article-title":"Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications","volume":"10","author":"Blacklock","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref122","doi-asserted-by":"crossref","first-page":"e1005159","DOI":"10.1371\/journal.pcbi.1005159","article-title":"Long-range signaling in MutS and MSH homologs via switching of dynamic communication pathways","volume":"12","author":"Wang","year":"2016","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref123","doi-asserted-by":"crossref","first-page":"2623","DOI":"10.1021\/acs.jcim.5b00454","article-title":"Molecular mechanism underlying PRMT1 dimerization for SAM binding and methylase activity","volume":"55","author":"Zhou","year":"2015","journal-title":"J Chem Inf Model"},{"key":"2020051819280779800_ref124","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1042\/BST20150283","article-title":"Structure network analysis to gain insights into GPCR function","volume":"44","author":"Fanelli","year":"2016","journal-title":"Biochem Soc Trans"},{"key":"2020051819280779800_ref125","doi-asserted-by":"crossref","first-page":"3131","DOI":"10.1016\/j.bbagen.2017.09.005","article-title":"Identification of potential allosteric communication pathways between functional sites of the bacterial ribosome by graph and elastic network models","volume":"1861","author":"Guzel","year":"2017","journal-title":"Biochim Biophys Acta Gen Subj"},{"key":"2020051819280779800_ref126","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.jtbi.2014.01.023","article-title":"Residue interaction network analysis of Dronpa and a DNA clamp","volume":"348","author":"Hu","year":"2014","journal-title":"J Theor Biol"},{"key":"2020051819280779800_ref127","doi-asserted-by":"crossref","first-page":"2367","DOI":"10.1016\/j.bbagen.2017.05.018","article-title":"Dissecting intrinsic and ligand-induced structural communication in the \u03b23 headpiece of integrins","volume":"1861","author":"Felline","year":"2017","journal-title":"Biochim Biophys Acta Gen Subj"},{"key":"2020051819280779800_ref128","doi-asserted-by":"crossref","first-page":"106327","DOI":"10.1039\/C6RA18243G","article-title":"Use of network model to explore dynamic and allosteric properties of three GPCR homodimers","volume":"6","author":"Jiang","year":"2016","journal-title":"RSC Adv"},{"key":"2020051819280779800_ref129","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1016\/j.bbagen.2018.04.015","article-title":"Deciphering the role of dimer interface in intrinsic dynamics and allosteric pathways underlying the functional transformation of DNMT3A","volume":"1862","author":"Liang","year":"2018","journal-title":"Biochim Biophys Acta Gen Subj"},{"key":"2020051819280779800_ref130","doi-asserted-by":"crossref","first-page":"e1003624","DOI":"10.1371\/journal.pcbi.1003624","article-title":"ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones","volume":"10","author":"General","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref131","doi-asserted-by":"crossref","first-page":"121","DOI":"10.2174\/1389203711314020004","article-title":"The topology and dynamics of protein complexes: insights from intra-molecular network theory","volume":"14","author":"Hu","year":"2013","journal-title":"Curr Protein Pept Sci"},{"key":"2020051819280779800_ref132","doi-asserted-by":"crossref","first-page":"37721","DOI":"10.1074\/jbc.M111.246702","article-title":"Allosteric communication in cysteinyl tRNA synthetase: a network of direct and indirect readout","volume":"286","author":"Ghosh","year":"2011","journal-title":"J Biol Chem"},{"key":"2020051819280779800_ref133","doi-asserted-by":"crossref","first-page":"e1003744","DOI":"10.1371\/journal.pcbi.1003744","article-title":"Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops","volume":"10","author":"Invernizzi","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref134","doi-asserted-by":"crossref","first-page":"e1004500","DOI":"10.1371\/journal.pcbi.1004500","article-title":"Mechanism of iron-dependent repressor (IdeR) activation and DNA binding: a molecular dynamics and protein structure network study","volume":"11","author":"Ghosh","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref135","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1021\/acs.jcim.7b00073","article-title":"Allosteric autoinhibition pathway in transcription factor ERG: dynamics network and mutant experimental evaluations","volume":"57","author":"Ye","year":"2017","journal-title":"J Chem Inf Model"},{"key":"2020051819280779800_ref136","first-page":"9096","article-title":"DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions","volume":"44","author":"Lambrughi","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2020051819280779800_ref137","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1039\/C4SC01320D","article-title":"Rational coupled dynamics network manipulation rescues disease-relevant mutant cystic fibrosis transmembrane conductance regulator","volume":"6","author":"Proctor","year":"2015","journal-title":"Chem Sci"},{"key":"2020051819280779800_ref138","doi-asserted-by":"crossref","first-page":"7294","DOI":"10.1038\/srep07294","article-title":"Global connectivity of hub residues in oncoprotein structures encodes genetic factors dictating personalized drug response to targeted cancer therapy","volume":"4","author":"Soundararajan","year":"2014","journal-title":"Sci Rep"},{"key":"2020051819280779800_ref139","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.gheart.2017.01.009","article-title":"Role of structural bioinformatics in drug discovery by computational SNP analysis: analyzing variation at the protein level","volume":"12","author":"Brown","year":"2017","journal-title":"Glob Heart"},{"key":"2020051819280779800_ref140","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/s12918-016-0382-0","article-title":"Network topology of NaV1.7 mutations in sodium channel-related painful disorders","volume":"11","author":"Kapetis","year":"2017","journal-title":"BMC Syst Biol"},{"key":"2020051819280779800_ref141","doi-asserted-by":"crossref","first-page":"e1002661","DOI":"10.1371\/journal.pcbi.1002661","article-title":"Allosteric communication across the native and mutated KIT receptor tyrosine kinase","volume":"8","author":"Laine","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref142","doi-asserted-by":"crossref","first-page":"e1003749","DOI":"10.1371\/journal.pcbi.1003749","article-title":"Hotspot mutations in KIT receptor differentially modulate its allosterically coupled conformational dynamics: impact on activation and drug sensitivity","volume":"10","author":"Chauvot","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref143","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1039\/C5MB00246J","article-title":"Small-world networks of residue interactions in the Abl kinase complexes with cancer drugs: topology of allosteric communication pathways can determine drug resistance effects","volume":"11","author":"Tse","year":"2015","journal-title":"Mol Biosyst"},{"key":"2020051819280779800_ref144","doi-asserted-by":"crossref","first-page":"3146","DOI":"10.1039\/C6MB00298F","article-title":"Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation","volume":"12","author":"Verkhivker","year":"2016","journal-title":"Mol Biosyst"},{"key":"2020051819280779800_ref145","doi-asserted-by":"crossref","first-page":"e166583","DOI":"10.1371\/journal.pone.0166583","article-title":"Exploring molecular mechanisms of paradoxical activation in the BRAF kinase dimers: atomistic simulations of conformational dynamics and modeling of allosteric communication networks and signaling pathways","volume":"11","author":"Tse","year":"2016","journal-title":"PLoS One"},{"key":"2020051819280779800_ref146","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1021\/acs.jcim.7b00638","article-title":"Functional role and hierarchy of the intermolecular interactions in binding of protein kinase clients to the Hsp90-Cdc37 chaperone: structure-based network modeling of allosteric regulation","volume":"58","author":"Stetz","year":"2018","journal-title":"J Chem Inf Model"},{"key":"2020051819280779800_ref147","doi-asserted-by":"crossref","first-page":"e1003207","DOI":"10.1371\/journal.pcbi.1003207","article-title":"Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases","volume":"9","author":"Mariani","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"2020051819280779800_ref148","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1002\/prot.24748","article-title":"Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association","volume":"83","author":"Butler","year":"2015","journal-title":"Proteins"},{"key":"2020051819280779800_ref149","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1016\/j.bpj.2015.06.060","article-title":"The role of conformational dynamics and allostery in the disease development of human ferritin","volume":"109","author":"Kumar","year":"2015","journal-title":"Biophys J"},{"key":"2020051819280779800_ref150","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1093\/bib\/bbx006","article-title":"Molecular dynamics recipes for genome research","volume":"19","author":"Biagini","year":"2018","journal-title":"Brief Bioinform"},{"key":"2020051819280779800_ref151","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1093\/molbev\/mss097","article-title":"Sequence evolution correlates with structural dynamics","volume":"29","author":"Liu","year":"2012","journal-title":"Mol Biol Evol"},{"key":"2020051819280779800_ref152","doi-asserted-by":"crossref","first-page":"2681","DOI":"10.1093\/bioinformatics\/btu336","article-title":"Evol and ProDy for bridging protein sequence evolution and structural dynamics","volume":"30","author":"Bakan","year":"2014","journal-title":"Bioinformatics"},{"key":"2020051819280779800_ref153","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1186\/s12859-014-0399-6","article-title":"Integrating protein structural dynamics and evolutionary analysis with Bio3D","volume":"15","author":"Skj\u00e6rven","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2020051819280779800_ref154","doi-asserted-by":"crossref","first-page":"3510","DOI":"10.1093\/bioinformatics\/btw482","article-title":"Online interactive analysis of protein structure ensembles with Bio3D-web","volume":"32","author":"Skj\u00e6rven","year":"2016","journal-title":"Bioinformatics"},{"key":"2020051819280779800_ref155","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1016\/j.str.2016.03.008","article-title":"Identifying allosteric hotspots with dynamics: application to inter- and intra-species conservation","volume":"24","author":"Clarke","year":"2016","journal-title":"Structure"},{"key":"2020051819280779800_ref156","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1002\/pro.3329","article-title":"Combining protein sequence, structure, and dynamics: a novel approach for functional evolution analysis of PAS domain superfamily","volume":"27","author":"Dong","year":"2018","journal-title":"Protein Sci"},{"key":"2020051819280779800_ref157","doi-asserted-by":"crossref","first-page":"1845","DOI":"10.1021\/acs.jctc.6b00049","article-title":"HTMD: high-throughput molecular dynamics for molecular discovery","volume":"12","author":"Doerr","year":"2016","journal-title":"J Chem Theory Comput"},{"key":"2020051819280779800_ref158","doi-asserted-by":"crossref","first-page":"241726","DOI":"10.1063\/1.5022469","article-title":"Machine learning approaches to evaluate correlation patterns in allosteric signaling: a case study of the PDZ2 domain","volume":"148","author":"Botlani","year":"2018","journal-title":"J Chem Phys"},{"key":"2020051819280779800_ref159","doi-asserted-by":"crossref","first-page":"64","DOI":"10.2174\/1568026611313010007","article-title":"Allo-network drugs: extension of the allosteric drug concept to protein\u2013protein interaction and signaling networks","volume":"13","author":"Szil\u00e1gyi","year":"2013","journal-title":"Curr Top Med Chem"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/21\/3\/815\/33227481\/bbz029.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/21\/3\/815\/33227481\/bbz029.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,13]],"date-time":"2023-09-13T22:17:26Z","timestamp":1694643446000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/21\/3\/815\/5393244"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3,21]]},"references-count":159,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2019,3,21]]},"published-print":{"date-parts":[[2020,5,21]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbz029","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2020,5]]},"published":{"date-parts":[[2019,3,21]]}}}