{"id":"https://openalex.org/W3087424893","doi":"https://doi.org/10.1371/journal.pcbi.1008103","title":"Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination","display_name":"Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination","publication_year":2020,"publication_date":"2020-09-21","ids":{"openalex":"https://openalex.org/W3087424893","doi":"https://doi.org/10.1371/journal.pcbi.1008103","mag":"3087424893","pmid":"https://pubmed.ncbi.nlm.nih.gov/32956350"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008103","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008103","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.1008103","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039852173","display_name":"Ryan E. Pavlovicz","orcid":"https://orcid.org/0000-0003-2446-3141"},"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":"Ryan E. Pavlovicz","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-2446-3141","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011280743","display_name":"Hahnbeom Park","orcid":"https://orcid.org/0000-0002-7129-1912"},"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":"Hahnbeom Park","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5105925656","display_name":"Frank DiMaio","orcid":null},"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":"Frank DiMaio","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5105925656"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.4275,"has_fulltext":false,"cited_by_count":64,"citation_normalized_percentile":{"value":0.93717308,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"16","issue":"9","first_page":"e1008103","last_page":"e1008103"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"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":1.0,"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":0.9997000098228455,"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/T11124","display_name":"Protein purification and stability","score":0.9962000250816345,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.8012185096740723},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.6720288991928101},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.6360158324241638},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.5702443718910217},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5225005745887756},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5148886442184448},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4958218038082123},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.4917609989643097},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.47529470920562744},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4111471176147461},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3898473083972931},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.37137484550476074},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.36517852544784546},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.35058140754699707},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.34235358238220215},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.20639857649803162},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16758817434310913},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.11654219031333923},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11260160803794861}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8012185096740723},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.6720288991928101},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.6360158324241638},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5702443718910217},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5225005745887756},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5148886442184448},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4958218038082123},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.4917609989643097},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.47529470920562744},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4111471176147461},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3898473083972931},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.37137484550476074},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.36517852544784546},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.35058140754699707},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.34235358238220215},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.20639857649803162},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16758817434310913},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.11654219031333923},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11260160803794861},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","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":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1008103","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008103","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:32956350","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32956350","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:RePEc:plo:pcbi00:1008103","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008103","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:9e24e11abd22477eae8e053fee934b3a","is_oa":true,"landing_page_url":"https://doaj.org/article/9e24e11abd22477eae8e053fee934b3a","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 16, Iss 9, p e1008103 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7529342","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7529342","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008103","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008103","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":[{"score":0.5899999737739563,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[{"id":"https://openalex.org/G2275473426","display_name":null,"funder_award_id":"GM123089","funder_id":"https://openalex.org/F4320337432","funder_display_name":"Center for Scientific Review"},{"id":"https://openalex.org/G602363890","display_name":null,"funder_award_id":"GM123089","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332622","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54"},{"id":"https://openalex.org/F4320337432","display_name":"Center for Scientific Review","ror":"https://ror.org/04r5s4b52"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1772371743","https://openalex.org/W1967850897","https://openalex.org/W1978809115","https://openalex.org/W1983194490","https://openalex.org/W1988437166","https://openalex.org/W1993807234","https://openalex.org/W2000702472","https://openalex.org/W2014693209","https://openalex.org/W2034533838","https://openalex.org/W2037320233","https://openalex.org/W2047730466","https://openalex.org/W2052466177","https://openalex.org/W2067236515","https://openalex.org/W2071827681","https://openalex.org/W2081719547","https://openalex.org/W2101993641","https://openalex.org/W2103994532","https://openalex.org/W2105417856","https://openalex.org/W2111387452","https://openalex.org/W2128494768","https://openalex.org/W2129954993","https://openalex.org/W2132629607","https://openalex.org/W2133712572","https://openalex.org/W2137841449","https://openalex.org/W2143598945","https://openalex.org/W2145310386","https://openalex.org/W2162083477","https://openalex.org/W2167207610","https://openalex.org/W2201713963","https://openalex.org/W2311078281","https://openalex.org/W2323927982","https://openalex.org/W2334483166","https://openalex.org/W2538176089","https://openalex.org/W2606439133","https://openalex.org/W2609454166","https://openalex.org/W2911679003","https://openalex.org/W2915344963"],"related_works":["https://openalex.org/W1581147483","https://openalex.org/W1974422922","https://openalex.org/W2005817231","https://openalex.org/W3187431608","https://openalex.org/W2331956508","https://openalex.org/W2885308902","https://openalex.org/W4309353019","https://openalex.org/W2078959398","https://openalex.org/W2031553931","https://openalex.org/W1997409847"],"abstract_inverted_index":{"Highly":[0],"coordinated":[1,63],"water":[2,29,50,84],"molecules":[3,30],"are":[4,52],"frequently":[5],"an":[6,16],"integral":[7],"part":[8],"of":[9,26,34,71,116],"protein-protein":[10,117],"and":[11,90,97,106,118],"protein-ligand":[12,119],"interfaces.":[13],"We":[14,100],"introduce":[15],"updated":[17],"energy":[18,107],"model":[19,85,108],"that":[20,102],"efficiently":[21],"captures":[22],"the":[23,32,69],"energetic":[24],"effects":[25],"these":[27],"ordered":[28],"on":[31,68],"surfaces":[33],"proteins.":[35],"A":[36],"two-stage":[37],"method":[38],"is":[39,86,91],"developed":[40],"in":[41,46,88,112],"which":[42],"polar":[43],"groups":[44],"arranged":[45],"geometries":[47],"suitable":[48,92],"for":[49,93],"placement":[51],"first":[53],"identified,":[54],"then":[55],"a":[56,72],"modified":[57],"Monte":[58],"Carlo":[59],"simulation":[60],"allows":[61],"highly":[62],"waters":[64],"to":[65],"be":[66],"placed":[67],"surface":[70],"protein":[73,98],"while":[74],"simultaneously":[75],"sampling":[76],"amino":[77],"acid":[78],"side":[79],"chain":[80],"orientations.":[81],"This":[82],"\"semi-explicit\"":[83],"implemented":[87],"Rosetta":[89],"both":[94],"structure":[95,114],"prediction":[96],"design.":[99],"show":[101],"our":[103],"new":[104],"approach":[105],"yield":[109],"significant":[110],"improvements":[111],"native":[113],"recovery":[115],"docking":[120],"discrimination":[121],"tests.":[122]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}