{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T10:50:55Z","timestamp":1767178255464,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007855","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,6,9]],"date-time":"2020-06-09T00:00:00Z","timestamp":1591660800000}}],"reference-count":75,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2020,5,14]],"date-time":"2020-05-14T00:00:00Z","timestamp":1589414400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007855","type":"journal-article","created":{"date-parts":[[2020,5,14]],"date-time":"2020-05-14T17:36:48Z","timestamp":1589477808000},"page":"e1007855","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Shape-preserving elastic solid models of macromolecules"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5153-6695","authenticated-orcid":true,"given":"Guang","family":"Song","sequence":"first","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,5,14]]},"reference":[{"issue":"1","key":"pcbi.1007855.ref001","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1007855.ref002","doi-asserted-by":"crossref","first-page":"1905","DOI":"10.1103\/PhysRevLett.77.1905","article-title":"Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis","volume":"77","author":"MM Tirion","year":"1996","journal-title":"Phys Rev Lett"},{"issue":"3","key":"pcbi.1007855.ref003","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/S1359-0278(97)00024-2","article-title":"Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential","volume":"2","author":"I Bahar","year":"1997","journal-title":"Fold Des"},{"issue":"3","key":"pcbi.1007855.ref004","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1002\/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8","article-title":"Analysis of domain motions by approximate normal mode calculations","volume":"33","author":"K Hinsen","year":"1998","journal-title":"Proteins"},{"issue":"1","key":"pcbi.1007855.ref005","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/S0006-3495(01)76033-X","article-title":"Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model","volume":"80","author":"AR Atilgan","year":"2001","journal-title":"Biophys J"},{"issue":"1","key":"pcbi.1007855.ref006","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/protein\/14.1.1","article-title":"Conformational change of proteins arising from normal mode calculations","volume":"14","author":"F Tama","year":"2001","journal-title":"Protein Eng"},{"issue":"1","key":"pcbi.1007855.ref007","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/1097-0134(20001001)41:1<1::AID-PROT10>3.0.CO;2-P","article-title":"Building-block approach for determining low-frequency normal modes of macromolecules","volume":"41","author":"F Tama","year":"2000","journal-title":"Proteins"},{"key":"pcbi.1007855.ref008","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1146\/annurev.biophys.35.040405.102010","article-title":"Symmetry, form, and shape: guiding principles for robustness in macromolecular machines","volume":"35","author":"F Tama","year":"2006","journal-title":"Annu Rev Biophys Biomol Struct"},{"issue":"5","key":"pcbi.1007855.ref009","doi-asserted-by":"crossref","first-page":"2123","DOI":"10.1021\/acs.jctc.7b00197","article-title":"NOLB: Nonlinear Rigid Block Normal-Mode Analysis Method","volume":"13","author":"A Hoffmann","year":"2017","journal-title":"J Chem Theory Comput"},{"issue":"4","key":"pcbi.1007855.ref010","doi-asserted-by":"crossref","first-page":"046003","DOI":"10.1088\/1478-3975\/aab813","article-title":"Fast Normal Mode Computations of Capsid Dynamics Inspired by Resonance","volume":"15","author":"H Na","year":"2018","journal-title":"Phys Biol"},{"issue":"9","key":"pcbi.1007855.ref011","doi-asserted-by":"crossref","first-page":"e1006456","DOI":"10.1371\/journal.pcbi.1006456","article-title":"All-atom normal mode dynamics of HIV-1 capsid","volume":"14","author":"H Na","year":"2018","journal-title":"PLoS Comput Biol"},{"issue":"11","key":"pcbi.1007855.ref012","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/bioinformatics\/btr168","article-title":"ProDy: protein dynamics inferred from theory and experiments","volume":"27","author":"A Bakan","year":"2011","journal-title":"Bioinformatics"},{"issue":"20","key":"pcbi.1007855.ref013","doi-asserted-by":"crossref","first-page":"2843","DOI":"10.1093\/bioinformatics\/btr497","article-title":"iMod: multipurpose normal mode analysis in internal coordinates","volume":"27","author":"JR Lopez-Blanco","year":"2011","journal-title":"Bioinformatics"},{"key":"pcbi.1007855.ref014","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.sbi.2018.11.005","article-title":"Advances in coarse-grained modeling of macromolecular complexes","volume":"52","author":"AJ Pak","year":"2018","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi.1007855.ref015","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.sbi.2015.11.013","article-title":"New generation of elastic network models","volume":"37","author":"JR Lopez-Blanco","year":"2016","journal-title":"Curr Opin Struct Biol"},{"issue":"2","key":"pcbi.1007855.ref016","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1002\/prot.10486","article-title":"Functional motions can be extracted from on-lattice construction of protein structures","volume":"53","author":"P Doruker","year":"2003","journal-title":"Proteins"},{"issue":"4","key":"pcbi.1007855.ref017","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1529\/biophysj.105.065904","article-title":"The role of shape in determining molecular motions","volume":"89","author":"M Lu","year":"2005","journal-title":"Biophys J"},{"issue":"4","key":"pcbi.1007855.ref018","doi-asserted-by":"crossref","first-page":"046003","DOI":"10.1088\/1478-3975\/ab1051","article-title":"Symmetry considerations elucidate the roles of global shape and local interactions in the equilibrium fluctuations and cooperativity of protein assemblies","volume":"16","author":"G Song","year":"2019","journal-title":"Phys Biol"},{"issue":"1","key":"pcbi.1007855.ref019","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1145\/174462.156635","article-title":"Three-dimensional alpha shapes","volume":"13","author":"H Edelsbrunner","year":"1994","journal-title":"ACM Transactions on Graphics"},{"issue":"4","key":"pcbi.1007855.ref020","doi-asserted-by":"crossref","first-page":"1595","DOI":"10.1002\/prot.21708","article-title":"A finite element framework for computation of protein normal modes and mechanical response","volume":"70","author":"M Bathe","year":"2008","journal-title":"Proteins"},{"issue":"4","key":"pcbi.1007855.ref021","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1093\/bioinformatics\/btm625","article-title":"Structural flexibility in proteins: impact of the crystal environment","volume":"24","author":"K Hinsen","year":"2008","journal-title":"Bioinformatics"},{"key":"pcbi.1007855.ref022","unstructured":"Hinsen K. The stuff that proteins are made of: physical properties of folded peptide chains. A research presentation. 2017. Available at https:\/\/www.youtube.com\/watch?v=RbOu1Vjp3Mc."},{"issue":"3","key":"pcbi.1007855.ref023","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1002\/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y","article-title":"Reduced surface: an efficient way to compute molecular surfaces","volume":"38","author":"MF Sanner","year":"1996","journal-title":"Biopolymers"},{"key":"pcbi.1007855.ref024","doi-asserted-by":"crossref","unstructured":"Garland M, Heckbert PS. Surface simplification using quadric error metrics. In: Proceedings of the 24th annual conference on computer graphics and interactive techniques (SIGGRAPH). Los Angeles, CA; 1997. p. 209\u2013216.","DOI":"10.1145\/258734.258849"},{"issue":"2","key":"pcbi.1007855.ref025","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/S0022-2836(02)00627-7","article-title":"Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory","volume":"321","author":"F Tama","year":"2002","journal-title":"J Mol Biol"},{"issue":"13","key":"pcbi.1007855.ref026","doi-asserted-by":"crossref","first-page":"8620","DOI":"10.1073\/pnas.082148899","article-title":"How to describe protein motion without amino acid sequence and atomic coordinates","volume":"99","author":"D Ming","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"pcbi.1007855.ref027","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1016\/j.str.2014.01.004","article-title":"Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes","volume":"22","author":"QY Jin","year":"2014","journal-title":"Structure"},{"issue":"2","key":"pcbi.1007855.ref028","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/S0022-2836(02)01426-2","article-title":"Mega-Dalton biomolecular motion captured from electron microscopy reconstructions","volume":"326","author":"P Chacon","year":"2003","journal-title":"J Mol Biol"},{"issue":"2-3","key":"pcbi.1007855.ref029","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1006\/jsbi.1998.4080","article-title":"Situs: A package for docking crystal structures into low-resolution maps from electron microscopy","volume":"125","author":"W Wriggers","year":"1999","journal-title":"J Struct Biol"},{"issue":"2-3","key":"pcbi.1007855.ref030","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1006\/jsbi.2000.4350","article-title":"Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data","volume":"133","author":"W Wriggers","year":"2001","journal-title":"Journal of Structural Biology"},{"issue":"1","key":"pcbi.1007855.ref031","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1109\/JSTSP.2015.2489186","article-title":"Coarse-Graining of Volumes for Modeling of Structure and Dynamics in Electron Microscopy: Algorithm to Automatically Control Accuracy of Approximation","volume":"10","author":"S Jonic","year":"2016","journal-title":"Ieee Journal of Selected Topics in Signal Processing"},{"issue":"2","key":"pcbi.1007855.ref032","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.jsb.2018.07.014","article-title":"A methodology using Gaussian-based density map approximation to assess sets of cryo-electron microscopy density maps","volume":"204","author":"S Jonic","year":"2018","journal-title":"Journal of Structural Biology"},{"issue":"8","key":"pcbi.1007855.ref033","doi-asserted-by":"crossref","first-page":"4359","DOI":"10.1039\/C8CP07442A","article-title":"A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes","volume":"21","author":"DV Anand","year":"2019","journal-title":"Physical Chemistry Chemical Physics"},{"issue":"13","key":"pcbi.1007855.ref034","doi-asserted-by":"crossref","first-page":"7151","DOI":"10.1016\/j.amc.2011.08.043","article-title":"Fast MATLAB assembly of FEM matrices in 2D and 3D: Nodal elements","volume":"219","author":"T Rahman","year":"2013","journal-title":"Applied Mathematics and Computation"},{"issue":"4","key":"pcbi.1007855.ref035","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1007\/BF01758770","article-title":"Randomized Incremental Construction of Delaunay and Voronoi Diagrams","volume":"7","author":"LJ Guibas","year":"1992","journal-title":"Algorithmica"},{"key":"pcbi.1007855.ref036","volume-title":"A first course in the finite element method","author":"DL Logan","year":"2007"},{"key":"pcbi.1007855.ref037","volume-title":"Mechanics of motor proteins and the cytoskeleton","author":"J Howard","year":"2001"},{"issue":"1","key":"pcbi.1007855.ref038","doi-asserted-by":"crossref","first-page":"012714","DOI":"10.1103\/PhysRevE.89.012714","article-title":"Elastic constants in orthorhombic hen egg-white lysozyme crystals","volume":"89","author":"N Kitajima","year":"2014","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"issue":"6 Pt 1","key":"pcbi.1007855.ref039","doi-asserted-by":"crossref","first-page":"061917","DOI":"10.1103\/PhysRevE.79.061917","article-title":"Elastic constants in tetragonal hen egg-white lysozyme crystals containing large amount of water","volume":"79","author":"H Koizumi","year":"2009","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"issue":"20","key":"pcbi.1007855.ref040","doi-asserted-by":"crossref","first-page":"7600","DOI":"10.1073\/pnas.0308198101","article-title":"Bacteriophage capsids: tough nanoshells with complex elastic properties","volume":"101","author":"IL Ivanovska","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"pcbi.1007855.ref041","first-page":"577","article-title":"Mechanical properties of globular proteins","volume":"17","author":"VN Morozov","year":"1983","journal-title":"Mol Biol (Mosk)"},{"issue":"1","key":"pcbi.1007855.ref042","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1016\/S0006-3495(00)76313-2","article-title":"Protein compressibility, dynamics, and pressure","volume":"79","author":"DP Kharakoz","year":"2000","journal-title":"Biophys J"},{"issue":"16","key":"pcbi.1007855.ref043","doi-asserted-by":"crossref","first-page":"6184","DOI":"10.1073\/pnas.0601744103","article-title":"Nanoindentation studies of full and empty viral capsids and the effects of capsid protein mutations on elasticity and strength","volume":"103","author":"JP Michel","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"Pt 1","key":"pcbi.1007855.ref044","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1107\/S0907444994009261","article-title":"The influence of temperature on lysozyme crystals. Structure and dynamics of protein and water","volume":"51","author":"IV Kurinov","year":"1995","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"issue":"5","key":"pcbi.1007855.ref045","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/j.sbi.2003.09.013","article-title":"\u2019Cool\u2019 crystals: macromolecular cryocrystallography and radiation damage","volume":"13","author":"E Garman","year":"2003","journal-title":"Curr Opin Struct Biol"},{"issue":"12","key":"pcbi.1007855.ref046","doi-asserted-by":"crossref","first-page":"5618","DOI":"10.1021\/ct400399x","article-title":"Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions","volume":"9","author":"E Fuglebakk","year":"2013","journal-title":"J Chem Theory Comput"},{"issue":"2","key":"pcbi.1007855.ref047","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1002\/prot.24735","article-title":"Conventional NMA as a better standard for evaluating elastic network models","volume":"83","author":"H Na","year":"2015","journal-title":"Proteins"},{"issue":"1","key":"pcbi.1007855.ref048","doi-asserted-by":"crossref","first-page":"016008","DOI":"10.1088\/1478-3975\/13\/1\/016008","article-title":"Universality of vibrational spectra of globular proteins","volume":"13","author":"H Na","year":"2016","journal-title":"Phys Biol"},{"issue":"Pt 5","key":"pcbi.1007855.ref049","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1107\/S0907444998002303","article-title":"Structure of pig plasma retinol-binding protein at 1.65 A resolution","volume":"54","author":"G Zanotti","year":"1998","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"issue":"3","key":"pcbi.1007855.ref050","doi-asserted-by":"crossref","first-page":"1903","DOI":"10.1016\/S0006-3495(03)74618-9","article-title":"Low-frequency modes of peptides and globular proteins in solution observed by ultrafast OHD-RIKES spectroscopy","volume":"85","author":"G Giraud","year":"2003","journal-title":"Biophys J"},{"issue":"21","key":"pcbi.1007855.ref051","doi-asserted-by":"crossref","first-page":"14559","DOI":"10.1103\/PhysRevB.47.14559","article-title":"Vibrational normal-mode spectrum of globular proteins","volume":"47","author":"D ben-Avraham","year":"1993","journal-title":"Phys Rev B"},{"key":"pcbi.1007855.ref052","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1038\/nature12162","article-title":"Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics","author":"G Zhao","year":"2013","journal-title":"Nature"},{"issue":"6243","key":"pcbi.1007855.ref053","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1126\/science.aaa5936","article-title":"X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability","volume":"349","author":"AT Gres","year":"2015","journal-title":"Science"},{"issue":"20","key":"pcbi.1007855.ref054","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.00845-18","article-title":"PF74 Reinforces the HIV-1 Capsid To Impair Reverse Transcription-Induced Uncoating","volume":"92","author":"S Rankovic","year":"2018","journal-title":"J Virol"},{"issue":"9","key":"pcbi.1007855.ref055","doi-asserted-by":"crossref","first-page":"3424","DOI":"10.1529\/biophysj.107.120733","article-title":"Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models","volume":"94","author":"E Eyal","year":"2008","journal-title":"Biophys J"},{"issue":"8","key":"pcbi.1007855.ref056","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1016\/j.bpj.2017.03.004","article-title":"Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change","volume":"112","author":"J Liu","year":"2017","journal-title":"Biophys J"},{"issue":"1","key":"pcbi.1007855.ref057","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/S0969-2126(01)00135-6","article-title":"Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy","volume":"3","author":"JA Speir","year":"1995","journal-title":"Structure"},{"issue":"1","key":"pcbi.1007855.ref058","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1002\/jcc.1160","article-title":"Dynamics of large proteins through hierarchical levels of coarse-grained structures","volume":"23","author":"P Doruker","year":"2002","journal-title":"J Comp Chem"},{"key":"pcbi.1007855.ref059","first-page":"279","article-title":"Fast and memory efficient polygonal simplification","author":"P Lindstrom","year":"1998","journal-title":"Visualization\u201998, Proceedings"},{"issue":"2","key":"pcbi.1007855.ref060","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1109\/2945.773803","article-title":"Evaluation of memoryless simplification","volume":"5","author":"P Lindstrom","year":"1999","journal-title":"IEEE Transactions on Visualization and Computer Graphics"},{"key":"pcbi.1007855.ref061","unstructured":"The CGAL Project. CGAL User and Reference Manual. 5.0 ed. CGAL Editorial Board; 2019. Available from: https:\/\/doc.cgal.org\/5.0\/Manual\/packages.html."},{"key":"pcbi.1007855.ref062","doi-asserted-by":"crossref","unstructured":"Jacobson A, Panozzo D, et al. libigl: A simple C++ geometry processing library; 2018.","DOI":"10.1145\/3134472.3134497"},{"key":"pcbi.1007855.ref063","volume-title":"ACM Transactions on Mathematical Software","author":"H Si","year":"2015"},{"issue":"11","key":"pcbi.1007855.ref064","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1002\/nme.2579","article-title":"Gmsh: A 3-D finite element mesh generator with built-in pre- and post-processing facilities","volume":"79","author":"C Geuzaine","year":"2009","journal-title":"International Journal for Numerical Methods in Engineering"},{"issue":"3","key":"pcbi.1007855.ref065","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1007\/s10514-013-9327-2","article-title":"Comparing ICP variants on real-world data sets","volume":"34","author":"F Pomerleau","year":"2013","journal-title":"Autonomous Robots"},{"issue":"D1","key":"pcbi.1007855.ref066","doi-asserted-by":"crossref","first-page":"D396","DOI":"10.1093\/nar\/gkv1126","article-title":"EMDataBank unified data resource for 3DEM","volume":"44","author":"CL Lawson","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"15","key":"pcbi.1007855.ref067","doi-asserted-by":"crossref","first-page":"6852","DOI":"10.1073\/pnas.1000232107","article-title":"Structure of lactococcal phage p2 baseplate and its mechanism of activation","volume":"107","author":"G Sciara","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"13","key":"pcbi.1007855.ref068","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2013a visualization system for exploratory research and analysis","volume":"25","author":"EF Pettersen","year":"2004","journal-title":"J Comput Chem"},{"issue":"1","key":"pcbi.1007855.ref069","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1002\/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H","article-title":"Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins","volume":"33","author":"J Liang","year":"1998","journal-title":"Proteins"},{"issue":"1","key":"pcbi.1007855.ref070","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O","article-title":"Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape","volume":"33","author":"J Liang","year":"1998","journal-title":"Proteins"},{"key":"pcbi.1007855.ref071","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1002\/prot.24571","article-title":"Bridging between normal mode analysis and elastic network models","volume":"82","author":"H Na","year":"2014","journal-title":"Proteins"},{"key":"pcbi.1007855.ref072","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/267585a0","article-title":"Dynamics of folded proteins","volume":"267","author":"JA McCammon","year":"1977","journal-title":"Nature"},{"key":"pcbi.1007855.ref073","first-page":"181","article-title":"The Normal Modes of a protein: Native bovine Pancreatic Trypsin inhibitor","volume":"10","author":"M Levitt","year":"1983","journal-title":"Int J Quant Chem"},{"issue":"12","key":"pcbi.1007855.ref074","doi-asserted-by":"crossref","first-page":"3696","DOI":"10.1073\/pnas.80.12.3696","article-title":"Dynamics of a small globular protein in terms of low-frequency vibrational modes","volume":"80","author":"N Go","year":"1983","journal-title":"Proc Natl Acad Sci USA"},{"issue":"21","key":"pcbi.1007855.ref075","doi-asserted-by":"crossref","first-page":"6571","DOI":"10.1073\/pnas.80.21.6571","article-title":"Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor","volume":"80","author":"B Brooks","year":"1983","journal-title":"Proc Natl Acad Sci USA"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007855","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,6,9]],"date-time":"2020-06-09T00:00:00Z","timestamp":1591660800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007855","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,9]],"date-time":"2020-06-09T13:59:13Z","timestamp":1591711153000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007855"}},"subtitle":[],"editor":[{"given":"Turkan","family":"Haliloglu","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,5,14]]},"references-count":75,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2020,5,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007855","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,5,14]]}}}