{"id":"https://openalex.org/W1980858273","doi":"https://doi.org/10.1371/journal.pcbi.1002505","title":"Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks","display_name":"Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks","publication_year":2012,"publication_date":"2012-05-17","ids":{"openalex":"https://openalex.org/W1980858273","doi":"https://doi.org/10.1371/journal.pcbi.1002505","mag":"1980858273","pmid":"https://pubmed.ncbi.nlm.nih.gov/22615547"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1002505","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002505","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1002505","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016171735","display_name":"M. S. Vijayabaskar","orcid":"https://orcid.org/0000-0002-5559-9394"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"M. S. Vijayabaskar","raw_affiliation_strings":["Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India","Molecular Biophysics Unit, Indian Institute of Science Bangalore India"],"affiliations":[{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India","institution_ids":["https://openalex.org/I59270414"]},{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science Bangalore India","institution_ids":["https://openalex.org/I59270414"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031607667","display_name":"Saraswathi Vishveshwara","orcid":"https://orcid.org/0000-0002-5035-7433"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Saraswathi Vishveshwara","raw_affiliation_strings":["Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India","Molecular Biophysics Unit, Indian Institute of Science Bangalore India"],"affiliations":[{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India","institution_ids":["https://openalex.org/I59270414"]},{"raw_affiliation_string":"Molecular Biophysics Unit, Indian Institute of Science Bangalore India","institution_ids":["https://openalex.org/I59270414"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5031607667"],"corresponding_institution_ids":["https://openalex.org/I59270414"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.3134,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.7855217,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"8","issue":"5","first_page":"e1002505","last_page":"e1002505"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9901999831199646,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9631999731063843,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5774288177490234},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.5175139904022217},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5020668506622314},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.488312691450119},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4874558448791504},{"id":"https://openalex.org/keywords/loop-modeling","display_name":"Loop modeling","score":0.4794025123119354},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.46902716159820557},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.42267102003097534},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.40830880403518677},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3812423050403595},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.31363511085510254},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.3072679042816162},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3068926930427551},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10223302245140076}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5774288177490234},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.5175139904022217},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5020668506622314},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.488312691450119},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4874558448791504},{"id":"https://openalex.org/C45475804","wikidata":"https://www.wikidata.org/wiki/Q6675846","display_name":"Loop modeling","level":4,"score":0.4794025123119354},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.46902716159820557},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.42267102003097534},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.40830880403518677},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3812423050403595},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.31363511085510254},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3072679042816162},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3068926930427551},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10223302245140076},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014305","descriptor_name":"Triose-Phosphate Isomerase","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D014305","descriptor_name":"Triose-Phosphate Isomerase","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D014305","descriptor_name":"Triose-Phosphate Isomerase","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D014305","descriptor_name":"Triose-Phosphate Isomerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014305","descriptor_name":"Triose-Phosphate Isomerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014305","descriptor_name":"Triose-Phosphate Isomerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1002505","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002505","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:22615547","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22615547","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:7d767ac614ce45e099e0aa5088a30f2c","is_oa":true,"landing_page_url":"https://doaj.org/article/7d767ac614ce45e099e0aa5088a30f2c","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 8, Iss 5, p e1002505 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2361463","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3355060","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/125022","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Insights_into_the_Fold_Organization_of_TIM_Barrel_from_Interaction_Energy_Based_Structure_Networks/125022","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1002505","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002505","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1508885706","https://openalex.org/W1535745346","https://openalex.org/W1604980477","https://openalex.org/W1838294703","https://openalex.org/W1971655977","https://openalex.org/W1975460133","https://openalex.org/W1977538576","https://openalex.org/W1989929509","https://openalex.org/W1991356723","https://openalex.org/W1991764480","https://openalex.org/W1992502768","https://openalex.org/W1996680929","https://openalex.org/W2000236879","https://openalex.org/W2000621476","https://openalex.org/W2008708467","https://openalex.org/W2011235285","https://openalex.org/W2013844611","https://openalex.org/W2015642465","https://openalex.org/W2019189533","https://openalex.org/W2020944535","https://openalex.org/W2022058405","https://openalex.org/W2024755629","https://openalex.org/W2031901496","https://openalex.org/W2045777307","https://openalex.org/W2057272352","https://openalex.org/W2060791849","https://openalex.org/W2062926294","https://openalex.org/W2073213802","https://openalex.org/W2075422720","https://openalex.org/W2075451741","https://openalex.org/W2076854887","https://openalex.org/W2083586651","https://openalex.org/W2083975423","https://openalex.org/W2085277871","https://openalex.org/W2092006899","https://openalex.org/W2093976897","https://openalex.org/W2095237995","https://openalex.org/W2095420958","https://openalex.org/W2102033493","https://openalex.org/W2109520948","https://openalex.org/W2117584882","https://openalex.org/W2121704271","https://openalex.org/W2130460395","https://openalex.org/W2145358391","https://openalex.org/W2150300758","https://openalex.org/W2151457629","https://openalex.org/W2152193893","https://openalex.org/W2156125289","https://openalex.org/W2159733730","https://openalex.org/W2163641424","https://openalex.org/W2167832495","https://openalex.org/W2169239268","https://openalex.org/W2170117113","https://openalex.org/W2170380686","https://openalex.org/W2171268876","https://openalex.org/W3019365222","https://openalex.org/W3145128584","https://openalex.org/W7029321148"],"related_works":["https://openalex.org/W3204091482","https://openalex.org/W2059079931","https://openalex.org/W2253761889","https://openalex.org/W2157930580","https://openalex.org/W1543174845","https://openalex.org/W2081601977","https://openalex.org/W2969133412","https://openalex.org/W4211156111","https://openalex.org/W2414840205","https://openalex.org/W1595347157"],"abstract_inverted_index":{"There":[0],"are":[1],"many":[2],"well-known":[3],"examples":[4],"of":[5,18,34,65,98,108,123,137,170,186,257,268],"proteins":[6],"with":[7,30],"low":[8],"sequence":[9,129,225],"similarity,":[10],"adopting":[11],"the":[12,35,44,63,78,88,105,111,121,124,133,138,161,164,179,183,187,244,248,253,266],"same":[13],"structural":[14,200,236],"fold.":[15,91,112],"This":[16],"aspect":[17],"sequence-structure":[19],"relationship":[20],"has":[21],"been":[22,192],"extensively":[23],"studied":[24],"both":[25,199,235],"experimentally":[26],"and":[27,82,149,201,237,252,271],"theoretically,":[28],"however":[29],"limited":[31],"success.":[32],"Most":[33],"studies":[36],"consider":[37],"remote":[38,218],"homology":[39],"or":[40,163],"\"sequence":[41],"conservation\"":[42,250],"as":[43],"basis":[45],"for":[46,120,217],"their":[47,83,196],"understanding.":[48],"Recently":[49],"\"interaction":[50,249],"energy\"":[51],"based":[52,214,226],"network":[53,213,259],"formalism":[54],"(Protein":[55],"Energy":[56],"Networks":[57],"(PENs))":[58],"was":[59],"developed":[60,95,210,255],"to":[61,76,103,167],"understand":[62,104],"determinants":[64],"protein":[66,275],"structures.":[67],"In":[68],"this":[69],"paper":[70],"we":[71,208],"have":[72,93,114,190,209],"used":[73],"these":[74,206],"PENs":[75,100],"investigate":[77],"common":[79,117],"non-covalent":[80],"interactions":[81,109,118,148,153,177],"collective":[84],"features":[85],"which":[86,220],"stabilize":[87],"TIM":[89,125,139,188],"barrel":[90,136],"We":[92,113,241],"also":[94,191],"a":[96,211],"method":[97,256],"aligning":[99],"in":[101,110,154,178,198,265],"order":[102],"spatial":[106],"conservation":[107,122],"identified":[115],"key":[116],"responsible":[119],"fold,":[126],"despite":[127],"high":[128,145,172],"dissimilarity.":[130],"For":[131],"instance,":[132],"central":[134],"beta":[135],"fold":[140,189,269],"is":[141,231],"stabilized":[142],"by":[143],"long-range":[144],"energy":[146,173],"electrostatic":[147],"low-energy":[150],"contiguous":[151],"vdW":[152],"certain":[155],"families.":[156],"The":[157],"other":[158],"interfaces":[159],"like":[160],"helix-sheet":[162],"helix-helix":[165],"seem":[166],"be":[168],"devoid":[169],"any":[171],"conserved":[174],"interactions.":[175],"Conserved":[176],"loop":[180],"regions":[181],"around":[182],"catalytic":[184],"site":[185],"identified,":[193],"pointing":[194],"out":[195],"significance":[197],"functional":[202,238],"evolution.":[203],"Based":[204],"on":[205],"investigations,":[207],"novel":[212],"phylogenetic":[215],"analysis":[216,230],"homologues,":[219],"can":[221,261],"perform":[222],"better":[223],"than":[224],"phylogeny.":[227],"Such":[228],"an":[229],"more":[232],"meaningful":[233],"from":[234],"evolutionary":[239],"perspective.":[240],"believe":[242],"that":[243],"information":[245],"obtained":[246],"through":[247],"viewpoint":[251],"subsequently":[254],"structure":[258],"alignment,":[260],"shed":[262],"new":[263],"light":[264],"fields":[267],"organization":[270],"de":[272],"novo":[273],"computational":[274],"design.":[276]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
