{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T21:23:21Z","timestamp":1743110601122,"version":"3.40.3"},"publisher-location":"Cham","reference-count":70,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030179342"},{"type":"electronic","value":"9783030179359"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1007\/978-3-030-17935-9_23","type":"book-chapter","created":{"date-parts":[[2019,4,30]],"date-time":"2019-04-30T12:49:05Z","timestamp":1556628545000},"page":"245-258","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Deciphering General Characteristics of Residues Constituting Allosteric Communication Paths"],"prefix":"10.1007","author":[{"given":"Girik","family":"Malik","sequence":"first","affiliation":[]},{"given":"Anirban","family":"Banerji","sequence":"additional","affiliation":[]},{"given":"Maksim","family":"Kouza","sequence":"additional","affiliation":[]},{"given":"Irina A.","family":"Buhimschi","sequence":"additional","affiliation":[]},{"given":"Andrzej","family":"Kloczkowski","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,4,13]]},"reference":[{"key":"23_CR1","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/S0022-2836(65)80285-6","volume":"12","author":"J Monod","year":"1965","unstructured":"Monod, J., Wyman, J., Changeux, J.P.: On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12, 88\u2013118 (1965)","journal-title":"J. Mol. Biol."},{"key":"23_CR2","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1021\/bi00865a047","volume":"5","author":"DE Koshland Jr","year":"1966","unstructured":"Koshland Jr., D.E., N\u00e9methy, G., Filmer, D.: Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5, 365\u2013385 (1966)","journal-title":"Biochemistry"},{"key":"23_CR3","doi-asserted-by":"publisher","first-page":"6263","DOI":"10.1021\/acs.chemrev.6b00283","volume":"116","author":"R Nussinov","year":"2016","unstructured":"Nussinov, R.: Introduction to protein ensembles and allostery. Chem. Rev. 116, 6263\u20136266 (2016)","journal-title":"Chem. Rev."},{"key":"23_CR4","doi-asserted-by":"publisher","first-page":"6488","DOI":"10.1021\/acs.chemrev.5b00543","volume":"116","author":"AA Ribeiro","year":"2016","unstructured":"Ribeiro, A.A., Ortiz, V.: A chemical perspective on allostery. Chem. Rev. 116, 6488\u20136502 (2016)","journal-title":"Chem. Rev."},{"key":"23_CR5","doi-asserted-by":"publisher","first-page":"6463","DOI":"10.1021\/acs.chemrev.5b00544","volume":"116","author":"NV Dokholyan","year":"2016","unstructured":"Dokholyan, N.V.: Controlling allosteric networks in proteins. Chem. Rev. 116, 6463\u20136487 (2016)","journal-title":"Chem. Rev."},{"key":"23_CR6","doi-asserted-by":"publisher","first-page":"6503","DOI":"10.1021\/acs.chemrev.5b00590","volume":"116","author":"J Guo","year":"2016","unstructured":"Guo, J., Zhou, H.X.: Protein allostery and conformational dynamics. Chem. Rev. 116, 6503\u20136515 (2016)","journal-title":"Chem. Rev."},{"key":"23_CR7","doi-asserted-by":"publisher","first-page":"6391","DOI":"10.1021\/acs.chemrev.5b00623","volume":"116","author":"E Papaleo","year":"2016","unstructured":"Papaleo, E., Saladino, G., Lambrughi, M., Lindorff-Larsen, K., Gervasio, F.L., Nussinov, R.: The role of protein loops and linkers in conformational dynamics and allostery. Chem. Rev. 116, 6391\u20136423 (2016)","journal-title":"Chem. Rev."},{"key":"23_CR8","doi-asserted-by":"publisher","first-page":"6516","DOI":"10.1021\/acs.chemrev.5b00562","volume":"116","author":"GH Wei","year":"2016","unstructured":"Wei, G.H., Xi, W.H., Nussinov, R., Ma, B.Y.: Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell. Chem. Rev. 116, 6516\u20136551 (2016)","journal-title":"Chem. Rev."},{"key":"23_CR9","doi-asserted-by":"publisher","first-page":"D510","DOI":"10.1093\/nar\/gkt1247","volume":"42","author":"ZM Huang","year":"2014","unstructured":"Huang, Z.M., Mou, L.K., Shen, Q.C., Lu, S.Y., Li, C.G., Liu, X.Y., et al.: ASD v2.0: updated content and novel features focusing on allosteric regulation. Nucleic Acids Res. 42, D510\u2013D516 (2014)","journal-title":"Nucleic Acids Res."},{"key":"23_CR10","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1002\/prot.21362","volume":"68","author":"YP Feng","year":"2007","unstructured":"Feng, Y.P., Kloczkowski, A., Jernigan, R.L.: Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys. Proteins 68, 57\u201366 (2007)","journal-title":"Proteins"},{"key":"23_CR11","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1002\/prot.22092","volume":"73","author":"Y Feng","year":"2008","unstructured":"Feng, Y., Jernigan, R.L., Kloczkowski, A.: Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron. Proteins 73, 730\u2013741 (2008)","journal-title":"Proteins"},{"key":"23_CR12","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1002\/prot.24454","volume":"82","author":"E Faraggi","year":"2014","unstructured":"Faraggi, E., Kloczkowski, A.: A global machine learning based scoring function for protein structure prediction. Proteins 82, 752\u2013759 (2014)","journal-title":"Proteins"},{"key":"23_CR13","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/1471-2105-15-22","volume":"15","author":"P Gniewek","year":"2014","unstructured":"Gniewek, P., Kolinski, A., Kloczkowski, A., Gront, D.: BioShell-threading: versatile Monte Carlo package for protein 3D threading. BMC Bioinform. 15, 22 (2014)","journal-title":"BMC Bioinform."},{"key":"23_CR14","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/bts243","volume":"28","author":"DL Theobald","year":"2012","unstructured":"Theobald, D.L., Steindel, P.A.: Optimal simultaneous superpositioning of multiple structures with missing data. Bioinformatics 28, 1972\u20131979 (2012)","journal-title":"Bioinformatics"},{"key":"23_CR15","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1080\/01621459.1937.10503522","volume":"32","author":"M Friedman","year":"1937","unstructured":"Friedman, M.: The use of ranks to avoid the assumption of normality implicit in the analysis of variance. J. Am. Stat. Assoc. 32, 675\u2013701 (1937). J. Am. Stat. Assoc. 34, 109 (1939)","journal-title":"J. Am. Stat. Assoc."},{"key":"23_CR16","doi-asserted-by":"publisher","first-page":"80","DOI":"10.2307\/3001968","volume":"1","author":"F Wilcoxon","year":"1945","unstructured":"Wilcoxon, F.: Individual comparisons by ranking methods. Biometrics Bull. 1, 80\u201383 (1945)","journal-title":"Biometrics Bull."},{"key":"23_CR17","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1214\/aoms\/1177731944","volume":"11","author":"M Friedman","year":"1940","unstructured":"Friedman, M.: A comparison of alternative tests of significance for the problem of m rankings. Ann. Math. Stat. 11, 86\u201392 (1940)","journal-title":"Ann. Math. Stat."},{"key":"23_CR18","doi-asserted-by":"publisher","first-page":"e0002051","DOI":"10.1371\/journal.pone.0002051","volume":"3","author":"MD Humphries","year":"2008","unstructured":"Humphries, M.D., Gurney, K.: Network \u2018small-world-ness\u2019: a quantitative method for determining canonical network equivalence. PLOS One 3, e0002051 (2008)","journal-title":"PLOS One"},{"key":"23_CR19","doi-asserted-by":"publisher","first-page":"W427","DOI":"10.1093\/nar\/gkt332","volume":"41","author":"M Jamroz","year":"2013","unstructured":"Jamroz, M., Kolinski, A., Kmiecik, S.: CABS-flex: server for fast simulation of protein structure fluctuations. Nucleic Acids Res. 41, W427\u2013W431 (2013)","journal-title":"Nucleic Acids Res."},{"key":"23_CR20","doi-asserted-by":"crossref","first-page":"349","DOI":"10.18388\/abp.2004_3575","volume":"51","author":"A Kolinski","year":"2004","unstructured":"Kolinski, A.: Protein modeling and structure prediction with a reduced representation. Acta Biochim. Pol. 51, 349\u2013371 (2004)","journal-title":"Acta Biochim. Pol."},{"key":"23_CR21","doi-asserted-by":"publisher","first-page":"7026","DOI":"10.1021\/jp301720w","volume":"116","author":"S Kmiecik","year":"2012","unstructured":"Kmiecik, S., Gront, D., Kouza, M., Kolinski, A.: From coarse-grained to atomic-level characterization of protein dynamics: transition state for the folding of B domain of protein A. J. Phys. Chem. B 116, 7026\u20137032 (2012)","journal-title":"J. Phys. Chem. B"},{"key":"23_CR22","doi-asserted-by":"publisher","first-page":"9893","DOI":"10.3390\/ijms14059893","volume":"14","author":"J Wabik","year":"2013","unstructured":"Wabik, J., Kmiecik, S., Gront, D., Kouza, M., Kolinski, A.: Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics. Int. J. Mol. Sci. 14, 9893\u20139905 (2013)","journal-title":"Int. J. Mol. Sci."},{"key":"23_CR23","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.ymeth.2015.07.004","volume":"93","author":"M Blaszczyk","year":"2016","unstructured":"Blaszczyk, M., Kurcinski, M., Kouza, M., Wieteska, L., Debinski, A., Kolinski, A., et al.: Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking. Methods 93, 72\u201383 (2016)","journal-title":"Methods"},{"key":"23_CR24","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1021\/ct300854w","volume":"9","author":"M Jamroz","year":"2013","unstructured":"Jamroz, M., Orozco, M., Kolinski, A., Kmiecik, S.: Consistent view of protein fluctuations from all-atom molecular dynamics and coarse-grained dynamics with knowledge-based force-field. J. Chem. Theory Comput. 9, 119\u2013125 (2013)","journal-title":"J. Chem. Theory Comput."},{"key":"23_CR25","doi-asserted-by":"publisher","first-page":"1593","DOI":"10.1002\/jcc.20624","volume":"28","author":"D Gront","year":"2007","unstructured":"Gront, D., Kmiecik, S., Kolinski, A.: Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. J. Comput. Chem. 28, 1593\u20131597 (2007)","journal-title":"J. Comput. Chem."},{"key":"23_CR26","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1007\/978-1-4939-0366-5_16","volume":"1137","author":"M Jamroz","year":"2014","unstructured":"Jamroz, M., Kolinski, A., Kmiecik, S.: Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model. Methods Mol. Biol. 1137, 235\u2013250 (2014)","journal-title":"Methods Mol. Biol."},{"key":"23_CR27","doi-asserted-by":"publisher","first-page":"e19238","DOI":"10.1371\/journal.pone.0019238","volume":"6","author":"WT Sun","year":"2011","unstructured":"Sun, W.T., He, J.: From isotropic to anisotropic side chain representations: comparison of three models for residue contact estimation. PLOS One 6, e19238  (2011)","journal-title":"PLOS One"},{"key":"23_CR28","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., et al.: The protein data bank. Nucleic Acids Res. 28, 235\u2013242 (2000)","journal-title":"Nucleic Acids Res."},{"key":"23_CR29","doi-asserted-by":"publisher","first-page":"7898","DOI":"10.1021\/acs.chemrev.6b00163","volume":"116","author":"S Kmiecik","year":"2016","unstructured":"Kmiecik, S., Gront, D., Kolinski, M., Wieteska, L., Dawid, A.E., Kolinski, A.: Coarse-grained protein models and their applications. Chem. Rev. 116, 7898\u20137936 (2016)","journal-title":"Chem. Rev."},{"key":"23_CR30","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1002\/prot.21652","volume":"71","author":"JI Sulkowska","year":"2008","unstructured":"Sulkowska, J.I., Kloczkowski, A., Sen, T.Z., Cieplak, M., Jernigan, R.L.: Predicting the order in which contacts are broken during single molecule protein stretching experiments. Proteins-Struct. Funct. Bioinform. 71, 45\u201360 (2008)","journal-title":"Proteins-Struct. Funct. Bioinform."},{"key":"23_CR31","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1146\/annurev.physchem.58.032806.104614","volume":"58","author":"HA Scheraga","year":"2007","unstructured":"Scheraga, H.A., Khalili, M., Liwo, A.: Protein-folding dynamics: overview of molecular simulation techniques. Annu. Rev. Phys. Chem. 58, 57\u201383 (2007)","journal-title":"Annu. Rev. Phys. Chem."},{"key":"23_CR32","doi-asserted-by":"publisher","first-page":"3518","DOI":"10.1021\/cr500638n","volume":"115","author":"J Nasica-Labouze","year":"2015","unstructured":"Nasica-Labouze, J., Nguyen, P.H., Sterpone, F., Berthoumieu, O., Buchete, N.V., Cote, S., et al.: Amyloid beta protein and Alzheimer\u2019s disease: when computer simulations complement experimental studies. Chem. Rev. 115, 3518\u20133563 (2015)","journal-title":"Chem. Rev."},{"key":"23_CR33","doi-asserted-by":"publisher","first-page":"145104","DOI":"10.1063\/1.4917073","volume":"142","author":"M Kouza","year":"2015","unstructured":"Kouza, M., Co, N.T., Nguyen, P.H., Kolinski, A., Li, M.S.: Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models. J. Chem. Phys. 142, 145104 (2015)","journal-title":"J. Chem. Phys."},{"key":"23_CR34","doi-asserted-by":"publisher","first-page":"2990","DOI":"10.1039\/C6CP07145G","volume":"19","author":"M Kouza","year":"2017","unstructured":"Kouza, M., Banerji, A., Kolinski, A., Buhimschi, I.A., Kloczkowski, A.: Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible model. Phys. Chem. Chem. Phys. 19, 2990\u20132999 (2017)","journal-title":"Phys. Chem. Chem. Phys."},{"key":"23_CR35","doi-asserted-by":"publisher","first-page":"3496","DOI":"10.3390\/ijms19113496","volume":"19","author":"S Kmiecik","year":"2018","unstructured":"Kmiecik, S., Kouza, M., Badaczewska-Dawid, A.E., Kloczkowski, A., Kolinski, A.: Modeling of protein structural flexibility and large-scale dynamics: coarse-grained simulations and elastic network models. Int. J. Mol. Sci. 19, 3496 (2018)","journal-title":"Int. J. Mol. Sci."},{"key":"23_CR36","doi-asserted-by":"publisher","first-page":"1995","DOI":"10.3390\/molecules23081995","volume":"23","author":"M Kouza","year":"2018","unstructured":"Kouza, M., Banerji, A., Kolinski, A., Buhimschi, I., Kloczkowski, A.: Role of resultant dipole moment in mechanical dissociation of biological complexes. Molecules 23, 1995 (2018)","journal-title":"Molecules"},{"key":"23_CR37","doi-asserted-by":"publisher","first-page":"215106","DOI":"10.1063\/1.5028575","volume":"148","author":"M Kouza","year":"2018","unstructured":"Kouza, M., Co, N.T., Li, M.S., Kmiecik, S., Kolinski, A., Kloczkowski, A., et al.: Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: a computational study. J. Chem. Phys. 148, 215106 (2018)","journal-title":"J. Chem. Phys."},{"key":"23_CR38","doi-asserted-by":"publisher","first-page":"175101","DOI":"10.1063\/1.5050483","volume":"149","author":"PD Lan","year":"2018","unstructured":"Lan, P.D., Kouza, M., Kloczkowski, A., Li, M.S.: A topological order parameter for describing folding free energy landscapes of proteins. J. Chem. Phys. 149, 175101 (2018)","journal-title":"J. Chem. Phys."},{"key":"23_CR39","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1021\/cr040425u","volume":"106","author":"E Shakhnovich","year":"2006","unstructured":"Shakhnovich, E.: Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem. Rev. 106, 1559\u20131588 (2006)","journal-title":"Chem. Rev."},{"key":"23_CR40","doi-asserted-by":"publisher","first-page":"16890","DOI":"10.1039\/c1cp20752k","volume":"13","author":"A Liwo","year":"2011","unstructured":"Liwo, A., He, Y., Scheraga, H.A.: Coarse-grained force field: general folding theory. Phys. Chem. Chem. Phys. 13, 16890\u201316901 (2011)","journal-title":"Phys. Chem. Chem. Phys."},{"key":"23_CR41","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1007\/s11693-013-9122-6","volume":"7","author":"A Banerji","year":"2013","unstructured":"Banerji, A.: An attempt to construct a (general) mathematical framework to model biological \u201ccontext-dependence\u201d. Syst. Synth. Biol. 7, 221\u2013227 (2013)","journal-title":"Syst. Synth. Biol."},{"key":"23_CR42","doi-asserted-by":"publisher","first-page":"1341","DOI":"10.1038\/nprot.2011.367","volume":"6","author":"N Tuncbag","year":"2011","unstructured":"Tuncbag, N., Gursoy, A., Nussinov, R., Keskin, O.: Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat. Protoc. 6, 1341\u20131354 (2011)","journal-title":"Nat. Protoc."},{"key":"23_CR43","first-page":"527","volume":"13","author":"SEA Ozbabacan","year":"2010","unstructured":"Ozbabacan, S.E.A., Gursoy, A., Keskin, O., Nussinov, R.: Conformational ensembles, signal transduction and residue hot spots: application to drug discovery. Curr. Opin. Drug Disc. 13, 527\u2013537 (2010)","journal-title":"Curr. Opin. Drug Disc."},{"key":"23_CR44","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","volume":"19","author":"H Akaike","year":"1974","unstructured":"Akaike, H.: A new look at the statistical-model identification. IEEE Trans. Autom. Control 19, 716\u2013723 (1974)","journal-title":"IEEE Trans. Autom. Control"},{"key":"23_CR45","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/0378-8733(78)90021-7","volume":"1","author":"LC Freeman","year":"1979","unstructured":"Freeman, L.C.: Centrality in social networks conceptual clarification. Soc. Netw. 1, 215\u2013239 (1979)","journal-title":"Soc. Netw."},{"key":"23_CR46","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/0378-8733(91)90017-N","volume":"13","author":"LC Freeman","year":"1991","unstructured":"Freeman, L.C., Borgatti, S.P., White, D.R.: Centrality in valued graphs - a measure of betweenness based on network flow. Soc. Netw. 13, 141\u2013154 (1991)","journal-title":"Soc. Netw."},{"key":"23_CR47","doi-asserted-by":"publisher","first-page":"016110","DOI":"10.1103\/PhysRevE.74.016110","volume":"74","author":"J Reichardt","year":"2006","unstructured":"Reichardt, J., Bornholdt, S.: Statistical mechanics of community detection. Phys. Rev. E 74, 016110 (2006)","journal-title":"Phys. Rev. E"},{"key":"23_CR48","doi-asserted-by":"publisher","first-page":"036115","DOI":"10.1103\/PhysRevE.80.036115","volume":"80","author":"VA Traag","year":"2009","unstructured":"Traag, V.A., Bruggeman, J.: Community detection in networks with positive and negative links. Phys. Rev. E 80, 036115   (2009)","journal-title":"Phys. Rev. E"},{"key":"23_CR49","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1006\/jmbi.1993.1074","volume":"229","author":"HM Grindley","year":"1993","unstructured":"Grindley, H.M., Artymiuk, P.J., Rice, D.W., Willett, P.: Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J. Mol. Biol. 229, 707\u2013721 (1993)","journal-title":"J. Mol. Biol."},{"key":"23_CR50","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1089\/cmb.1996.3.289","volume":"3","author":"I Koch","year":"1996","unstructured":"Koch, I., Lengauer, T., Wanke, E.: An algorithm for finding maximal common subtopologies in a set of protein structures. J. Comput. Biol. 3, 289\u2013306 (1996)","journal-title":"J. Comput. Biol."},{"key":"23_CR51","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1023\/A:1021271615909","volume":"16","author":"JW Raymond","year":"2002","unstructured":"Raymond, J.W., Willett, P.: Maximum common subgraph isomorphism algorithms for the matching of chemical structures. J. Comput. Aid. Mol. Des. 16, 521\u2013533 (2002)","journal-title":"J. Comput. Aid. Mol. Des."},{"key":"23_CR52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0304-3975(00)00286-3","volume":"250","author":"I Koch","year":"2001","unstructured":"Koch, I.: Enumerating all connected maximal common subgraphs in two graphs. Theor. Comput. Sci. 250, 1\u201330 (2001)","journal-title":"Theor. Comput. Sci."},{"key":"23_CR53","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1002\/spe.4380120103","volume":"12","author":"JJ McGregor","year":"1982","unstructured":"McGregor, J.J.: Backtrack search algorithms and the maximal common subgraph problem. Softw. Pract. Exp. 12, 23\u201334 (1982)","journal-title":"Softw. Pract. Exp."},{"key":"23_CR54","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1126\/science.286.5439.509","volume":"286","author":"AL Barabasi","year":"1999","unstructured":"Barabasi, A.L., Albert, R.: Emergence of scaling in random networks. Science 286, 509\u2013512 (1999)","journal-title":"Science"},{"key":"23_CR55","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/nrg1272","volume":"5","author":"AL Barabasi","year":"2004","unstructured":"Barabasi, A.L., Oltvai, Z.N.: Network biology: understanding the cell\u2019s functional organization. Nat. Rev. Genet. 5, 101\u2013113 (2004)","journal-title":"Nat. Rev. Genet."},{"key":"23_CR56","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1038\/30918","volume":"393","author":"DJ Watts","year":"1998","unstructured":"Watts, D.J., Strogatz, S.H.: Collective dynamics of \u2018small-world\u2019 networks. Nature 393, 440\u2013442 (1998)","journal-title":"Nature"},{"key":"23_CR57","doi-asserted-by":"publisher","first-page":"054101","DOI":"10.1103\/PhysRevLett.89.054101","volume":"89","author":"M Barahona","year":"2002","unstructured":"Barahona, M., Pecora, L.M.: Synchronization in small-world systems. Phys. Rev. Lett. 89, 054101 (2002)","journal-title":"Phys. Rev. Lett."},{"key":"23_CR58","doi-asserted-by":"publisher","first-page":"014101","DOI":"10.1103\/PhysRevLett.91.014101","volume":"91","author":"T Nishikawa","year":"2003","unstructured":"Nishikawa, T., Motter, A.E., Lai, Y.C., Hoppensteadt, F.C.: Heterogeneity in oscillator networks: are smaller worlds easier to synchronize? Phys. Rev. Lett. 91, 014101 (2003)","journal-title":"Phys. Rev. Lett."},{"key":"23_CR59","doi-asserted-by":"publisher","first-page":"198101","DOI":"10.1103\/PhysRevLett.92.198101","volume":"92","author":"A Roxin","year":"2004","unstructured":"Roxin, A., Riecke, H., Solla, S.A.: Self-sustained activity in a small-world network of excitable neurons. Phys. Rev. Lett. 92, 198101 (2004)","journal-title":"Phys. Rev. Lett."},{"key":"23_CR60","doi-asserted-by":"publisher","first-page":"2758","DOI":"10.1103\/PhysRevLett.84.2758","volume":"84","author":"LF Lago-Fernandez","year":"2000","unstructured":"Lago-Fernandez, L.F., Huerta, R., Corbacho, F., Siguenza, J.A.: Fast response and temporal coherent oscillations in small-world networks. Phys. Rev. Lett. 84, 2758\u20132761 (2000)","journal-title":"Phys. Rev. Lett."},{"key":"23_CR61","doi-asserted-by":"publisher","first-page":"672","DOI":"10.1002\/prot.20348","volume":"58","author":"A del Sol","year":"2005","unstructured":"del Sol, A., O\u2019Meara, P.: Small-world network approach to identify key residues in protein-protein interaction. Proteins 58, 672\u2013682 (2005)","journal-title":"Proteins"},{"key":"23_CR62","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1016\/j.str.2014.11.011","volume":"23","author":"H Kim","year":"2015","unstructured":"Kim, H., Zou, T.S., Modi, C., Dorner, K., Grunkemeyer, T.J., Chen, L.Q., et al.: A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins. Structure 23, 34\u201343 (2015)","journal-title":"Structure"},{"key":"23_CR63","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1007\/978-3-319-02970-2_5","volume":"805","author":"H Na","year":"2014","unstructured":"Na, H., Lin, T.L., Song, G.: Generalized spring tensor models for protein fluctuation dynamics and conformation changes. Adv. Exp. Med. Biol. 805, 107\u2013135 (2014)","journal-title":"Adv. Exp. Med. Biol."},{"key":"23_CR64","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1002\/prot.20836","volume":"63","author":"G Song","year":"2006","unstructured":"Song, G., Jernigan, R.L.: An enhanced elastic network model to represent the motions of domain-swapped proteins. Proteins 63, 197\u2013209 (2006)","journal-title":"Proteins"},{"key":"23_CR65","doi-asserted-by":"publisher","first-page":"1425","DOI":"10.1002\/prot.24040","volume":"80","author":"M Jamroz","year":"2012","unstructured":"Jamroz, M., Kolinski, A., Kihara, D.: Structural features that predict real-value fluctuations of globular proteins. Proteins 80, 1425\u20131435 (2012)","journal-title":"Proteins"},{"key":"23_CR66","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1002\/prot.22082","volume":"73","author":"YD Yang","year":"2008","unstructured":"Yang, Y.D., Park, C., Kihara, D.: Threading without optimizing weighting factors for scoring function. Proteins 73, 581\u2013596 (2008)","journal-title":"Proteins"},{"key":"23_CR67","doi-asserted-by":"publisher","first-page":"011912","DOI":"10.1103\/PhysRevE.71.011912","volume":"71","author":"MB Enright","year":"2005","unstructured":"Enright, M.B., Leitner, D.M.: Mass fractal dimension and the compactness of proteins. Phys. Rev. E 71, 011912 (2005)","journal-title":"Phys. Rev. E"},{"key":"23_CR68","doi-asserted-by":"publisher","first-page":"e7361","DOI":"10.1371\/journal.pone.0007361","volume":"4","author":"A Banerji","year":"2009","unstructured":"Banerji, A., Ghosh, I.: Revisiting the myths of protein interior: studying proteins with mass-fractal hydrophobicity-fractal and polarizability-fractal dimensions. PLOS One 4, e7361 (2009)","journal-title":"PLOS One"},{"key":"23_CR69","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1146\/annurev.physchem.59.032607.093606","volume":"59","author":"DM Leitner","year":"2008","unstructured":"Leitner, D.M.: Energy flow in proteins. Annu. Rev. Phys. Chem. 59, 233\u2013259 (2008)","journal-title":"Annu. Rev. Phys. Chem."},{"key":"23_CR70","doi-asserted-by":"publisher","first-page":"13696","DOI":"10.1073\/pnas.1002018107","volume":"107","author":"S Reuveni","year":"2010","unstructured":"Reuveni, S., Granek, R., Klafter, J.: Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure. Proc. Natl. Acad. Sci. U.S.A. 107, 13696\u201313700 (2010)","journal-title":"Proc. Natl. Acad. Sci. U.S.A."}],"container-title":["Lecture Notes in Computer Science","Bioinformatics and Biomedical Engineering"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-17935-9_23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,13]],"date-time":"2024-03-13T13:11:52Z","timestamp":1710335512000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-030-17935-9_23"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9783030179342","9783030179359"],"references-count":70,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-17935-9_23","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2019]]},"assertion":[{"value":"13 April 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"IWBBIO","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Work-Conference on Bioinformatics and Biomedical Engineering","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Granada","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Spain","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2019","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"8 May 2019","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"10 May 2019","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"7","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"iwbbio2019","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/iwbbio.ugr.es\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}