{"id":"https://openalex.org/W2105417856","doi":"https://doi.org/10.1002/prot.20347","title":"A \u201csolvated rotamer\u201d approach to modeling water\u2010mediated hydrogen bonds at protein\u2013protein interfaces","display_name":"A \u201csolvated rotamer\u201d approach to modeling water\u2010mediated hydrogen bonds at protein\u2013protein interfaces","publication_year":2005,"publication_date":"2005-01-13","ids":{"openalex":"https://openalex.org/W2105417856","doi":"https://doi.org/10.1002/prot.20347","mag":"2105417856","pmid":"https://pubmed.ncbi.nlm.nih.gov/15651050"},"language":"en","primary_location":{"id":"doi:10.1002/prot.20347","doi":"https://doi.org/10.1002/prot.20347","is_oa":false,"landing_page_url":"https://doi.org/10.1002/prot.20347","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018203421","display_name":"Lin Jiang","orcid":"https://orcid.org/0000-0003-3039-1877","observed_orcids":["https://orcid.org/0000-0003-3039-1877","https://orcid.org/0000-0002-3926-886X"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lin Jiang","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013989048","display_name":"Brian A. Kuhlman","orcid":"https://orcid.org/0000-0003-4907-9699","observed_orcids":["https://orcid.org/0000-0003-4907-9699"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Brian Kuhlman","raw_affiliation_strings":["University of North Carolina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000906927","display_name":"Tanja Kortemme","orcid":"https://orcid.org/0000-0002-8494-680X","observed_orcids":["https://orcid.org/0000-0002-8494-680X"]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tanja Kortemme","raw_affiliation_strings":["University of California at San Francisco,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California at San Francisco,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053192926","display_name":"David A. Baker","orcid":"https://orcid.org/0000-0001-7896-6217","observed_orcids":["https://orcid.org/0000-0001-7896-6217"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David Baker","raw_affiliation_strings":["Biomolecular Structure & Design Program, University of Washington, Seattle, Washington","Department of Biochemistry, University of Washington, Seattle, Washington","University of Washington"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomolecular Structure & Design Program, University of Washington, Seattle, Washington","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"University of Washington","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5053192926"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":4550,"currency":"USD","value_usd":4550},"apc_paid":null,"fwci":4.0156,"has_fulltext":false,"cited_by_count":139,"citation_normalized_percentile":{"value":0.94641049,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"58","issue":"4","first_page":"893","last_page":"904"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9976000189781189,"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":0.9976000189781189,"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":0.000699999975040555,"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"}},{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/water-mediated-hydrogen-bonds","display_name":"water-mediated hydrogen bonding","score":0.9950000047683716},{"id":"https://openalex.org/keywords/protein-protein-interfaces","display_name":"protein-protein interfaces","score":0.968999981880188},{"id":"https://openalex.org/keywords/buried-water-molecules","display_name":"buried water molecules","score":0.906000018119812},{"id":"https://openalex.org/keywords/free-energy-prediction","display_name":"free energy prediction","score":0.4790000021457672},{"id":"https://openalex.org/keywords/side-chain-packing","display_name":"side-chain packing","score":0.7950000166893005},{"id":"https://openalex.org/keywords/protein-stability","display_name":"protein stability","score":0.550000011920929}],"concepts":[{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.8208637237548828},{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.671889066696167},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.6081807613372803},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5380740761756897},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.5297499895095825},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5252040028572083},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5138649940490723},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.5005683898925781},{"id":"https://openalex.org/C166940927","wikidata":"https://www.wikidata.org/wiki/Q178827","display_name":"Monomer","level":3,"score":0.4950208067893982},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.4749586582183838},{"id":"https://openalex.org/C153064111","wikidata":"https://www.wikidata.org/wiki/Q1281033","display_name":"Protein crystallization","level":3,"score":0.46781229972839355},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.43087029457092285},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4229244589805603},{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.42191070318222046},{"id":"https://openalex.org/C2780471494","wikidata":"https://www.wikidata.org/wiki/Q146505","display_name":"Solvent","level":2,"score":0.4125458598136902},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1204192042350769},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.10077297687530518},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.09280717372894287},{"id":"https://openalex.org/C203036418","wikidata":"https://www.wikidata.org/wiki/Q284256","display_name":"Crystallization","level":2,"score":0.07894647121429443}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","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":false},{"descriptor_ui":"D009584","descriptor_name":"Nitrogen","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1002/prot.20347","doi":"https://doi.org/10.1002/prot.20347","is_oa":false,"landing_page_url":"https://doi.org/10.1002/prot.20347","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15651050","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15651050","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,"listed_in":[],"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":"Proteins","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1974909022","https://openalex.org/W1985724808","https://openalex.org/W1985907120","https://openalex.org/W2008380486","https://openalex.org/W2023003128","https://openalex.org/W2028231353","https://openalex.org/W2028843689","https://openalex.org/W2038222142","https://openalex.org/W2045501270","https://openalex.org/W2062029510","https://openalex.org/W2075770210","https://openalex.org/W2078362683","https://openalex.org/W2080528351","https://openalex.org/W2089878534","https://openalex.org/W2109539263","https://openalex.org/W2121954997","https://openalex.org/W2134059200","https://openalex.org/W2134636873","https://openalex.org/W2134731229","https://openalex.org/W2135815512","https://openalex.org/W2150192011","https://openalex.org/W2153153865","https://openalex.org/W2160085559"],"related_works":["https://openalex.org/W7095674890","https://openalex.org/W7095091065","https://openalex.org/W1975338077","https://openalex.org/W2066746009","https://openalex.org/W4387335280","https://openalex.org/W2159489787","https://openalex.org/W2073562226","https://openalex.org/W3087424893","https://openalex.org/W1974909022","https://openalex.org/W2091725428"],"abstract_inverted_index":{"Water-mediated":[0],"hydrogen":[1,37],"bonds":[2],"play":[3],"critical":[4],"roles":[5],"at":[6,67,98],"protein-protein":[7,68,99,140],"and":[8,12,39,70,101,114,139,143],"protein-nucleic":[9],"acid":[10,76,137],"interfaces,":[11,69],"the":[13,33,46,57,60,71,93,121,125,151],"interactions":[14],"formed":[15],"by":[16],"discrete":[17],"water":[18,50,96,127],"molecules":[19,51,128],"cannot":[20],"be":[21,130],"captured":[22],"using":[23],"continuum":[24],"solvent":[25],"models.":[26],"We":[27,83],"describe":[28,85],"a":[29,86],"simple":[30],"model":[31,58],"for":[32,146],"energetics":[34],"of":[35,45,48,62,73,95,135,150],"water-mediated":[36],"bonds,":[38],"show":[40],"that,":[41],"together":[42],"with":[43,108],"knowledge":[44],"positions":[47,94],"buried":[49],"observed":[52],"in":[53,78,102],"X-ray":[54],"crystal":[55],"structures,":[56],"improves":[59],"prediction":[61,134],"free-energy":[63],"changes":[64],"upon":[65],"mutation":[66],"recovery":[72],"native":[74],"amino":[75,136],"sequences":[77],"protein":[79,115],"interface":[80,141],"design":[81,116],"calculations.":[82],"then":[84],"\"solvated":[87],"rotamer\"":[88],"approach":[89],"to":[90,123,132],"efficiently":[91],"predict":[92],"molecules,":[97],"interfaces":[100],"monomeric":[103],"proteins,":[104],"that":[105],"is":[106],"compatible":[107],"widely":[109],"used":[110,131],"rotamer-based":[111],"side-chain":[112],"packing":[113],"algorithms.":[117],"Finally,":[118],"we":[119],"examine":[120],"extent":[122],"which":[124],"predicted":[126],"can":[129],"improve":[133],"identities":[138],"stability,":[142],"discuss":[144],"avenues":[145],"overcoming":[147],"current":[148],"limitations":[149],"approach.":[152]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":13}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
