{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T04:32:31Z","timestamp":1769315551815,"version":"3.49.0"},"reference-count":36,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2009,12,11]],"date-time":"2009-12-11T00:00:00Z","timestamp":1260489600000},"content-version":"unspecified","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.1000592","type":"journal-article","created":{"date-parts":[[2009,12,10]],"date-time":"2009-12-10T23:03:44Z","timestamp":1260486224000},"page":"e1000592","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":42,"title":["Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins"],"prefix":"10.1371","volume":"5","author":[{"given":"Orly","family":"Noivirt-Brik","sequence":"first","affiliation":[]},{"given":"Amnon","family":"Horovitz","sequence":"additional","affiliation":[]},{"given":"Ron","family":"Unger","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2009,12,11]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1126\/science.2392678","article-title":"De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence.","volume":"249","author":"MH Hecht","year":"1990","journal-title":"Science"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"10015","DOI":"10.1073\/pnas.94.19.10015","article-title":"Rational protein design: Combining theory and experiment.","volume":"94","author":"HW Hellinga","year":"1997","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1371\/journal.pcbi.0030052","article-title":"Positive and negative design in stability and thermal adaptation of natural proteins.","volume":"3","author":"IN Berezovsky","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1006\/jmbi.1998.1645","article-title":"Contact order, transition state placement and the refolding rates of single domain proteins.","volume":"277","author":"KW Plaxco","year":"1998","journal-title":"J Mol Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1002\/pro.5560040401","article-title":"Principles of protein folding\u2013a perspective from simple exact models.","volume":"4","author":"KA Dill","year":"1995","journal-title":"Protein Sci"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/369248a0","article-title":"How does a protein fold?","volume":"369","author":"A Sali","year":"1994","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1016\/S1359-0278(96)00060-0","article-title":"Protein folding funnels: the nature of the transition state ensemble.","volume":"1","author":"JN Onuchic","year":"1996","journal-title":"Fold & Des"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1006\/jmbi.1996.0375","article-title":"Local interactions dominate folding in a simple protein model.","volume":"259","author":"R Unger","year":"1996","journal-title":"J Mol Biol"},{"key":"ref9","first-page":"121","article-title":"Perspectives on protein evolution from simple exact models.","volume":"1","author":"HS Chan","year":"2002","journal-title":"Appl Bioinformatics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.sbi.2004.03.001","article-title":"Simulating protein evolution in sequence and structure space.","volume":"14","author":"Y Xia","year":"2004","journal-title":"Curr Opin Struct Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1146\/annurev.physchem.58.032806.104449","article-title":"Understanding protein evolution: from protein physics to Darwinian selection.","volume":"59","author":"KB Zeldovich","year":"2008","journal-title":"Annu Rev Phys Chem"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"R121","DOI":"10.1016\/S1359-0278(96)00056-9","article-title":"Double-mutant cycles: a powerful tool for analysing protein structure and function.","volume":"1","author":"A Horovitz","year":"1996","journal-title":"Fold & Des"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1472-6807-9-4","article-title":"Analysing the origin of long-range interactions in proteins using lattice models.","volume":"9","author":"O Noivirt-Brik","year":"2009","journal-title":"BMC Struct Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1063\/1.456500","article-title":"Intrachain loops in polymers: effects of excluded volume.","volume":"90","author":"HS Chan","year":"1989","journal-title":"J Chem Phys"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1002\/prot.340180402","article-title":"Correlated mutations and residue contacts in proteins.","volume":"18","author":"U G\u00f6bel","year":"1994","journal-title":"Proteins: Struct Funct Genet"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1073\/pnas.91.1.98","article-title":"How frequent are correlated changes in families of protein sequences?","volume":"91","author":"E Neher","year":"1994","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1126\/science.286.5438.295","article-title":"Evolutionarily conserved pathways of energetic connectivity in protein families.","volume":"286","author":"SW Lockless","year":"1999","journal-title":"Science"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1002\/prot.10180","article-title":"Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations.","volume":"48","author":"I Kass","year":"2002","journal-title":"Proteins: Struct Funct Genet"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1002\/prot.10074","article-title":"In silico two-hybrid system for the selection of physically interacting protein pairs.","volume":"47","author":"F Pazos","year":"2002","journal-title":"Proteins: Struct Funct Genet"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1073\/pnas.0805923106","article-title":"Identification of direct residue contacts in protein-protein interaction by message passing.","volume":"106","author":"M Weigt","year":"2009","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/nature03991","article-title":"Evolutionary information for specifying a protein fold.","volume":"437","author":"M Socolich","year":"2005","journal-title":"Nature"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"3288","DOI":"10.1073\/pnas.97.7.3288","article-title":"Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap.","volume":"97","author":"KR Wollenberg","year":"2000","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1002\/prot.20098","article-title":"Influence of conservation on calculations of amino acid covariance in multiple sequence alignments.","volume":"56","author":"AA Fodor","year":"2004","journal-title":"Proteins: Struct Funct Bioinf"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1093\/protein\/gzi029","article-title":"Detection and reduction of evolutionary noise in correlated mutation analysis.","volume":"18","author":"O Noivirt","year":"2005","journal-title":"Protein Eng Des Sel"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/j.cell.2005.05.028","article-title":"Proteome-wide analysis of chaperonin-dependent protein folding in <italic>Escherichia coli<\/italic>.","volume":"122","author":"MJ Kerner","year":"2005","journal-title":"Cell"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"12742","DOI":"10.1073\/pnas.0503890102","article-title":"Physics and evolution of thermophilic adaptation.","volume":"102","author":"IN Berezovsky","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.tig.2007.10.005","article-title":"Gaining and losing the thermophilic adaptation in prokaryotes.","volume":"24","author":"P Puigb\u00f2","year":"2007","journal-title":"Trends Genet"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.gene.2008.06.020","article-title":"How does gene expression level contribute to thermophilic adaptation of prokaryotes? An exploration based on predictors.","volume":"421","author":"J Wang","year":"2008","journal-title":"Gene"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1371\/journal.pcbi.0030005","article-title":"Protein and DNA sequence determinants of thermophilic adaptation.","volume":"3","author":"KB Zeldovich","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1063\/1.1699114","article-title":"Equation of state calculations by fast computing machines.","volume":"21","author":"N Metropolis","year":"1953","journal-title":"J Chem Phys"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"9343","DOI":"10.1021\/bi00492a006","article-title":"Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles.","volume":"29","author":"L Serrano","year":"1990","journal-title":"Biochemistry"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"D786","DOI":"10.1093\/nar\/gkl893","article-title":"DisProt: the Database of Disordered Proteins.","volume":"35","author":"M Sickmeier","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"D115","DOI":"10.1093\/nar\/gkh131","article-title":"UniProt: the Universal Protein knowledgebase.","volume":"32","author":"R Apweiler","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkj405","article-title":"Escherichia coli K-12: a cooperatively developed annotation snapshot-2005.","volume":"34","author":"M Riley","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.","volume":"22","author":"JD Thompson","year":"1994","journal-title":"Nucleic Acids Res"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000592","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T04:20:10Z","timestamp":1540268410000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000592"}},"subtitle":[],"editor":[{"given":"Jose","family":"Onuchic","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2009,12,11]]},"references-count":36,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2009,12,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000592","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,12,11]]}}}