{"id":"https://openalex.org/W1950772819","doi":"https://doi.org/10.1186/1471-2105-7-326","title":"A maximum likelihood framework for protein design","display_name":"A maximum likelihood framework for protein design","publication_year":2006,"publication_date":"2006-06-29","ids":{"openalex":"https://openalex.org/W1950772819","doi":"https://doi.org/10.1186/1471-2105-7-326","mag":"1950772819","pmid":"https://pubmed.ncbi.nlm.nih.gov/16808841"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-326","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-326","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-326","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-326","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033420524","display_name":"Claudia L. Kleinman","orcid":"https://orcid.org/0000-0002-5158-7126"},"institutions":[{"id":"https://openalex.org/I109736498","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95","country_code":"CA","type":"facility","lineage":["https://openalex.org/I109736498"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Claudia L Kleinman","raw_affiliation_strings":["Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada. cl.kleinman@umontreal.ca","Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada. cl.kleinman@umontreal.ca","institution_ids":["https://openalex.org/I109736498","https://openalex.org/I70931966"]},{"raw_affiliation_string":"Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec Canada","institution_ids":["https://openalex.org/I109736498","https://openalex.org/I70931966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014774866","display_name":"Nicolas Rodrigue","orcid":"https://orcid.org/0000-0002-6250-8876"},"institutions":[{"id":"https://openalex.org/I109736498","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95","country_code":"CA","type":"facility","lineage":["https://openalex.org/I109736498"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nicolas Rodrigue","raw_affiliation_strings":["Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada","Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I109736498","https://openalex.org/I70931966"]},{"raw_affiliation_string":"Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Canada","institution_ids":["https://openalex.org/I109736498","https://openalex.org/I70931966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025101116","display_name":"C\u00e9cile Bonnard","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"C\u00e9cile Bonnard","raw_affiliation_strings":["Laboratoire d'lnformatique, de Robotique et de Micro\u00e9lectronique de Montpellier, UMR 5506, CNRS-Universit\u00e9 de Montpellier 2, 161, rue Ada, 34392, Montpellier Cedex 5, France","Laboratoire d'lnformatique, de Robotique et de Micro\u00e9lectronique de Montpellier, UMR 5506, CNRS-Universit\u00e9 de Montpellier 2, Montpellier Cedex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire d'lnformatique, de Robotique et de Micro\u00e9lectronique de Montpellier, UMR 5506, CNRS-Universit\u00e9 de Montpellier 2, 161, rue Ada, 34392, Montpellier Cedex 5, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210101743"]},{"raw_affiliation_string":"Laboratoire d'lnformatique, de Robotique et de Micro\u00e9lectronique de Montpellier, UMR 5506, CNRS-Universit\u00e9 de Montpellier 2, Montpellier Cedex 5, France","institution_ids":["https://openalex.org/I4210101743","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101537273","display_name":"Herv\u00e9 Philippe","orcid":"https://orcid.org/0000-0002-1335-8015"},"institutions":[{"id":"https://openalex.org/I109736498","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95","country_code":"CA","type":"facility","lineage":["https://openalex.org/I109736498"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Herv\u00e9 Philippe","raw_affiliation_strings":["Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada","Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I109736498","https://openalex.org/I70931966"]},{"raw_affiliation_string":"Canadian Institute for Advanced Research, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Canada","institution_ids":["https://openalex.org/I109736498","https://openalex.org/I70931966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057909697","display_name":"Nicolas Lartillot","orcid":"https://orcid.org/0000-0002-9973-7760"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4405261681"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Nicolas Lartillot","raw_affiliation_strings":["Laboratoire d'lnformatique, de Robotique et de Micro\u00e9lectronique de Montpellier, UMR 5506, CNRS-Universit\u00e9 de Montpellier 2, 161, rue Ada, 34392, Montpellier Cedex 5, France","Laboratoire d'lnformatique, de Robotique et de Micro\u00e9lectronique de Montpellier, UMR 5506, CNRS-Universit\u00e9 de Montpellier 2, Montpellier Cedex 5, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire d'lnformatique, de Robotique et de Micro\u00e9lectronique de Montpellier, UMR 5506, CNRS-Universit\u00e9 de Montpellier 2, 161, rue Ada, 34392, Montpellier Cedex 5, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210101743"]},{"raw_affiliation_string":"Laboratoire d'lnformatique, de Robotique et de Micro\u00e9lectronique de Montpellier, UMR 5506, CNRS-Universit\u00e9 de Montpellier 2, Montpellier Cedex 5, France","institution_ids":["https://openalex.org/I4210101743","https://openalex.org/I19894307","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5057909697"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210101743"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.5,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.79880176,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"7","issue":"1","first_page":"326","last_page":"326"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9663000106811523,"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":0.9663000106811523,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.009100000374019146,"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":0.003599999938160181,"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.7338366508483887},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6406395435333252},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.617456316947937},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.49287867546081543},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.4542246162891388},{"id":"https://openalex.org/keywords/model-selection","display_name":"Model selection","score":0.45238471031188965},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3609238266944885},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.323729932308197},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.31663045287132263},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31480440497398376},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2534557282924652}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7338366508483887},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6406395435333252},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.617456316947937},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.49287867546081543},{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.4542246162891388},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.45238471031188965},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3609238266944885},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.323729932308197},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.31663045287132263},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31480440497398376},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2534557282924652},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"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":"D016503","descriptor_name":"Drug Delivery Systems","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016503","descriptor_name":"Drug Delivery Systems","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016503","descriptor_name":"Drug Delivery Systems","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},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/1471-2105-7-326","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-326","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-326","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16808841","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16808841","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:HAL:lirmm-00135040v1","is_oa":true,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-00135040","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"BMC Bioinformatics, 2006, 7, pp.326-336. ⟨10.1186/1471-2105-7-326⟩","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:d8b2445e6cb74512b40b061260ecbe70","is_oa":true,"landing_page_url":"https://doaj.org/article/d8b2445e6cb74512b40b061260ecbe70","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 7, Iss 1, p 326 (2006)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:353689","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1570151","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":"","raw_type":"Text"},{"id":"pmh:oai:papyrus.bib.umontreal.ca:1866/659","is_oa":true,"landing_page_url":"http://hdl.handle.net/1866/659","pdf_url":null,"source":{"id":"https://openalex.org/S4306402422","display_name":"Papyrus : Institutional Repository (Universit\u00e9 de Montr\u00e9al)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I70931966","host_organization_name":"Universit\u00e9 de Montr\u00e9al","host_organization_lineage":["https://openalex.org/I70931966"],"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":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1570151","is_oa":true,"landing_page_url":"http://doi.org/10.1186/1471-2105-7-326","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-326","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-326","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-326","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"},{"id":"https://openalex.org/F4320323175","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1950772819.pdf","grobid_xml":"https://content.openalex.org/works/W1950772819.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1490016045","https://openalex.org/W1547596077","https://openalex.org/W1574312817","https://openalex.org/W1589812083","https://openalex.org/W1975017420","https://openalex.org/W1981159651","https://openalex.org/W1984313562","https://openalex.org/W1994550454","https://openalex.org/W1995824897","https://openalex.org/W2001956250","https://openalex.org/W2003604086","https://openalex.org/W2004360551","https://openalex.org/W2008097610","https://openalex.org/W2011507824","https://openalex.org/W2013164703","https://openalex.org/W2023235722","https://openalex.org/W2027071679","https://openalex.org/W2033496784","https://openalex.org/W2034767804","https://openalex.org/W2035999724","https://openalex.org/W2037928576","https://openalex.org/W2038864914","https://openalex.org/W2039248602","https://openalex.org/W2040401984","https://openalex.org/W2041877620","https://openalex.org/W2042380360","https://openalex.org/W2045091067","https://openalex.org/W2049633694","https://openalex.org/W2053929098","https://openalex.org/W2058187117","https://openalex.org/W2059681116","https://openalex.org/W2060778016","https://openalex.org/W2062663912","https://openalex.org/W2072843928","https://openalex.org/W2074732152","https://openalex.org/W2081325432","https://openalex.org/W2082240576","https://openalex.org/W2085764610","https://openalex.org/W2087928415","https://openalex.org/W2092732430","https://openalex.org/W2093089891","https://openalex.org/W2093689899","https://openalex.org/W2096619551","https://openalex.org/W2098538101","https://openalex.org/W2103047198","https://openalex.org/W2105038759","https://openalex.org/W2116214348","https://openalex.org/W2121061814","https://openalex.org/W2124730634","https://openalex.org/W2131071247","https://openalex.org/W2135580377","https://openalex.org/W2153153865","https://openalex.org/W2160529747","https://openalex.org/W2165271176","https://openalex.org/W2169882791","https://openalex.org/W2171697750","https://openalex.org/W2908736965","https://openalex.org/W3101224382"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2942366970","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2562400057","https://openalex.org/W1692008701","https://openalex.org/W2597588799","https://openalex.org/W4360593462","https://openalex.org/W2188234385"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,159],"aim":[2],"of":[3,48,62,77,91,98,114,161,212,215,224,249,254,265],"protein":[4,93,280],"design":[5,94],"is":[6,147,153,164],"to":[7,66,109,124,171,207,219,230,244,275],"predict":[8],"amino-acid":[9],"sequences":[10],"compatible":[11],"with":[12,126,178],"a":[13,20,31,59,89,115,172,179,189,246],"given":[14],"target":[15],"structure.":[16],"Traditionally":[17],"envisioned":[18],"as":[19],"purely":[21],"thermodynamic":[22,157,266],"question,":[23,64],"this":[24,52,170,239],"problem":[25,95],"can":[26],"also":[27],"be":[28,231],"understood":[29],"in":[30,96,143],"wider":[32],"context,":[33],"where":[34],"additional":[35],"constraints":[36],"are":[37],"captured":[38],"by":[39,45,149,156,166],"learning":[40,70],"the":[41,63,75,92,105,111,145,162,185,199,209,216,221,263,277],"sequence":[42],"patterns":[43],"displayed":[44],"natural":[46],"proteins":[47],"known":[49],"conformation.":[50],"In":[51],"latter":[53],"perspective,":[54],"however,":[55],"we":[56,119],"still":[57],"need":[58],"theoretical":[60],"formalization":[61],"leading":[65],"general":[67],"and":[68,72,79,152,182,218,282],"efficient":[69],"methods,":[71],"allowing":[73],"for":[74,130,258],"selection":[76],"fast":[78],"accurate":[80],"objective":[81],"functions":[82],"quantifying":[83],"sequence/structure":[84],"compatibility.":[85],"RESULTS:":[86],"We":[87,133,168],"propose":[88,134],"formulation":[90],"terms":[97],"model-based":[99,270],"statistical":[100,116,271],"inference.":[101],"Our":[102],"framework":[103],"uses":[104],"maximum":[106],"likelihood":[107,146],"principle":[108],"optimize":[110],"unknown":[112],"parameters":[113],"potential,":[117,176,217],"which":[118,144,227],"call":[120],"an":[121,135],"inverse":[122],"potential":[123],"contrast":[125],"classical":[127],"potentials":[128],"used":[129],"structure":[131],"prediction.":[132],"implementation":[136],"based":[137],"on":[138],"Markov":[139],"chain":[140],"Monte":[141],"Carlo,":[142],"maximized":[148],"gradient":[150],"descent":[151],"numerically":[154],"estimated":[155],"integration.":[158],"fit":[160],"models":[163,187],"evaluated":[165],"cross-validation.":[167],"apply":[169],"simple":[173],"pairwise":[174,196],"contact":[175],"supplemented":[177],"solvent-accessibility":[180],"term,":[181],"show":[183],"that":[184],"resulting":[186],"have":[188],"better":[190],"predictive":[191],"power":[192],"than":[193,234,261],"currently":[194],"available":[195],"potentials.":[197],"Furthermore,":[198],"model":[200],"comparison":[201],"method":[202],"presented":[203],"here":[204],"allows":[205],"one":[206],"measure":[208],"relative":[210],"contribution":[211],"each":[213],"component":[214],"choose":[220],"optimal":[222],"number":[223],"accessibility":[225],"classes,":[226],"turns":[228],"out":[229],"much":[232],"higher":[233],"classically":[235],"considered.":[236],"CONCLUSION:":[237],"Altogether,":[238],"reformulation":[240],"makes":[241],"it":[242],"possible":[243],"test":[245],"wide":[247],"diversity":[248],"models,":[250],"using":[251],"different":[252],"forms":[253],"potentials,":[255],"or":[256],"accounting":[257],"other":[259],"factors":[260],"just":[262],"constraint":[264],"stability.":[267],"Ultimately,":[268],"such":[269],"analyses":[272],"may":[273],"help":[274],"understand":[276],"forces":[278],"shaping":[279],"sequences,":[281],"driving":[283],"their":[284],"evolution.":[285]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}