{"id":"https://openalex.org/W2073562226","doi":"https://doi.org/10.1021/ci200118y","title":"Modeling of the Water Network at Protein\u2013RNA Interfaces","display_name":"Modeling of the Water Network at Protein\u2013RNA Interfaces","publication_year":2011,"publication_date":"2011-05-25","ids":{"openalex":"https://openalex.org/W2073562226","doi":"https://doi.org/10.1021/ci200118y","mag":"2073562226","pmid":"https://pubmed.ncbi.nlm.nih.gov/21612274"},"language":"en","primary_location":{"id":"doi:10.1021/ci200118y","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200118y","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"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/A5048050760","display_name":"Yiyu Li","orcid":"https://orcid.org/0000-0001-9424-5524"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yiyu Li","raw_affiliation_strings":["Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, United States"],"affiliations":[{"raw_affiliation_string":"Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, United States","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000884943","display_name":"Brian T. Sutch","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian T. Sutch","raw_affiliation_strings":["Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, United States","Ligand Insight, LLC, Post Office Box 5731, Pasadena, California 91117, United States"],"affiliations":[{"raw_affiliation_string":"Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, United States","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Ligand Insight, LLC, Post Office Box 5731, Pasadena, California 91117, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076329672","display_name":"Huynh\u2010Hoa Bui","orcid":null},"institutions":[{"id":"https://openalex.org/I2800035258","display_name":"Ionis Pharmaceuticals (United States)","ror":"https://ror.org/00t8bew53","country_code":"US","type":"company","lineage":["https://openalex.org/I2800035258"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Huynh-Hoa Bui","raw_affiliation_strings":["Isis Pharmaceuticals Inc., 1896 Rutherford Road, Carlsbad, California 92008-7326, United States"],"affiliations":[{"raw_affiliation_string":"Isis Pharmaceuticals Inc., 1896 Rutherford Road, Carlsbad, California 92008-7326, United States","institution_ids":["https://openalex.org/I2800035258"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110259428","display_name":"Timothy K. Gallaher","orcid":null},"institutions":[{"id":"https://openalex.org/I4210141293","display_name":"Neumedicines (United States)","ror":"https://ror.org/050e4js82","country_code":"US","type":"company","lineage":["https://openalex.org/I4210141293"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy K. Gallaher","raw_affiliation_strings":["Neumedicines Inc., 2708 Foothill Boulevard, Suite #403, La Crescenta, California 91214, United States"],"affiliations":[{"raw_affiliation_string":"Neumedicines Inc., 2708 Foothill Boulevard, Suite #403, La Crescenta, California 91214, United States","institution_ids":["https://openalex.org/I4210141293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036618056","display_name":"Ian S. Haworth","orcid":"https://orcid.org/0000-0002-3873-0899"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ian S. Haworth","raw_affiliation_strings":["Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, United States"],"affiliations":[{"raw_affiliation_string":"Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, United States","institution_ids":["https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5048050760"],"corresponding_institution_ids":["https://openalex.org/I1174212"],"apc_list":null,"apc_paid":null,"fwci":0.97833348,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.7276731,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"51","issue":"6","first_page":"1347","last_page":"1352"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9994999766349792,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9927999973297119,"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/rna","display_name":"RNA","score":0.4978954792022705},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4344331622123718},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42501479387283325},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2851213216781616},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23059439659118652},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13711467385292053}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4978954792022705},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4344331622123718},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42501479387283325},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2851213216781616},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23059439659118652},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13711467385292053},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D009690","descriptor_name":"Nucleic Acid Conformation","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D009690","descriptor_name":"Nucleic Acid Conformation","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D009690","descriptor_name":"Nucleic Acid Conformation","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci200118y","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200118y","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:21612274","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21612274","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/6","display_name":"Clean water and sanitation","score":0.8500000238418579}],"awards":[],"funders":[{"id":"https://openalex.org/F4320308668","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1967747508","https://openalex.org/W1976623517","https://openalex.org/W1982030445","https://openalex.org/W1997945165","https://openalex.org/W2005647584","https://openalex.org/W2005739967","https://openalex.org/W2022154149","https://openalex.org/W2027192815","https://openalex.org/W2033490251","https://openalex.org/W2034882414","https://openalex.org/W2042928151","https://openalex.org/W2043218293","https://openalex.org/W2048770907","https://openalex.org/W2051167017","https://openalex.org/W2053208573","https://openalex.org/W2053538195","https://openalex.org/W2055400985","https://openalex.org/W2060683541","https://openalex.org/W2064515831","https://openalex.org/W2065009334","https://openalex.org/W2066311224","https://openalex.org/W2066746009","https://openalex.org/W2083519509","https://openalex.org/W2104529244","https://openalex.org/W2105417856","https://openalex.org/W2110304798","https://openalex.org/W2116489181","https://openalex.org/W2122406707","https://openalex.org/W2129954993","https://openalex.org/W2130479394","https://openalex.org/W2137271253","https://openalex.org/W2138866442","https://openalex.org/W2162000798"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Water":[0],"plays":[1],"an":[2,20,37],"important":[3,21],"role":[4],"in":[5,23,67,107],"the":[6,24,42,59,68,79,87,99,108,113,119,123,129],"mediation":[7],"of":[8,16,27,44,52,58,71,73,78,86,89,132],"biomolecular":[9],"interactions.":[10],"Thus,":[11],"accurate":[12],"prediction":[13,60],"and":[14,32,101,103],"evaluation":[15],"water-mediated":[17],"interactions":[18],"is":[19,61,82],"element":[22],"computational":[25,130],"design":[26,131],"interfaces":[28],"involving":[29],"proteins,":[30],"RNA,":[31],"DNA.":[33],"Here,":[34],"we":[35],"use":[36],"algorithm":[38],"(WATGEN)":[39],"to":[40,112],"predict":[41],"locations":[43],"interfacial":[45],"water":[46,64,80,91,124],"molecules":[47,65],"for":[48,121,126],"a":[49],"data":[50],"set":[51],"224":[53],"protein-RNA":[54,133],"interfaces.":[55],"The":[56,76],"accuracy":[57],"validated":[62],"against":[63],"present":[66],"X-ray":[69],"structures":[70],"105":[72],"these":[74],"complexes.":[75,134],"complexity":[77],"networks":[81],"deconvoluted":[83],"through":[84],"definition":[85],"characteristics":[88],"each":[90],"molecule":[92],"based":[93],"on":[94,104],"its":[95,105],"bridging":[96],"properties":[97],"between":[98],"protein":[100],"RNA":[102],"depth":[106],"interface":[109],"with":[110],"respect":[111],"bulk":[114],"solvent.":[115],"This":[116],"approach":[117],"has":[118],"potential":[120],"scoring":[122],"network":[125],"incorporation":[127],"into":[128]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
