{"id":"https://openalex.org/W2031168104","doi":"https://doi.org/10.1007/s10822-013-9644-8","title":"Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments","display_name":"Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments","publication_year":2013,"publication_date":"2013-03-01","ids":{"openalex":"https://openalex.org/W2031168104","doi":"https://doi.org/10.1007/s10822-013-9644-8","mag":"2031168104","pmid":"https://pubmed.ncbi.nlm.nih.gov/23579614"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-013-9644-8","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-013-9644-8","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","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/A5089550693","display_name":"G. Madhavi Sastry","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"G. Madhavi Sastry","raw_affiliation_strings":["Schr\u00f6dinger, Sanali Infopark, Banjara Hills, Hyderabad, Andhra Pradesh, India","Schr\u00f6dinger Hyderabad India"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Sanali Infopark, Banjara Hills, Hyderabad, Andhra Pradesh, India","institution_ids":[]},{"raw_affiliation_string":"Schr\u00f6dinger Hyderabad India","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004917027","display_name":"Matvey Adzhigirey","orcid":null},"institutions":[{"id":"https://openalex.org/I4210161498","display_name":"Schrodinger (United States)","ror":null,"country_code":"US","type":null,"lineage":["https://openalex.org/I4210161498"]},{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matvey Adzhigirey","raw_affiliation_strings":["Schr\u00f6dinger, 120 West 45th Street, New York, NY, 10036, USA","Schr\u00f6dinger, New York, USA"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, 120 West 45th Street, New York, NY, 10036, USA","institution_ids":["https://openalex.org/I4210161498"]},{"raw_affiliation_string":"Schr\u00f6dinger, New York, USA","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022073517","display_name":"Tyler Day","orcid":"https://orcid.org/0000-0001-9603-4341"},"institutions":[{"id":"https://openalex.org/I4210161498","display_name":"Schrodinger (United States)","ror":null,"country_code":"US","type":null,"lineage":["https://openalex.org/I4210161498"]},{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tyler Day","raw_affiliation_strings":["Schr\u00f6dinger, 120 West 45th Street, New York, NY, 10036, USA","Schr\u00f6dinger, New York, USA"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, 120 West 45th Street, New York, NY, 10036, USA","institution_ids":["https://openalex.org/I4210161498"]},{"raw_affiliation_string":"Schr\u00f6dinger, New York, USA","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026863167","display_name":"Ramakrishna Annabhimoju","orcid":null},"institutions":[{"id":"https://openalex.org/I4210119054","display_name":"Cancer Hospital and Research Institute","ror":"https://ror.org/01rhx3w79","country_code":"IN","type":"healthcare","lineage":["https://openalex.org/I4210119054"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Ramakrishna Annabhimoju","raw_affiliation_strings":["Schr\u00f6dinger, Sanali Infopark, 8-2-120/113, Banjara Hills, Hyderabad, 500034, Andhra Pradesh, India","Schr\u00f6dinger Hyderabad India"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Sanali Infopark, 8-2-120/113, Banjara Hills, Hyderabad, 500034, Andhra Pradesh, India","institution_ids":["https://openalex.org/I4210119054"]},{"raw_affiliation_string":"Schr\u00f6dinger Hyderabad India","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087455853","display_name":"Woody Sherman","orcid":"https://orcid.org/0000-0001-9079-1376"},"institutions":[{"id":"https://openalex.org/I4210161498","display_name":"Schrodinger (United States)","ror":null,"country_code":"US","type":null,"lineage":["https://openalex.org/I4210161498"]},{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Woody Sherman","raw_affiliation_strings":["Schr\u00f6dinger, 120 West 45th Street, New York, NY, 10036, USA","Schr\u00f6dinger, New York, USA"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, 120 West 45th Street, New York, NY, 10036, USA","institution_ids":["https://openalex.org/I4210161498"]},{"raw_affiliation_string":"Schr\u00f6dinger, New York, USA","institution_ids":["https://openalex.org/I203455613"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5089550693"],"corresponding_institution_ids":[],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":141.6593,"has_fulltext":false,"cited_by_count":5888,"citation_normalized_percentile":{"value":0.99993673,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"27","issue":"3","first_page":"221","last_page":"234"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.998199999332428,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9957000017166138,"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/virtual-screening","display_name":"Virtual screening","score":0.9330477118492126},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.648905336856842},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.46635687351226807},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3501153588294983},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.17680492997169495},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.132938414812088}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.9330477118492126},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.648905336856842},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.46635687351226807},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3501153588294983},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.17680492997169495},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.132938414812088},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[{"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":"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-013-9644-8","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-013-9644-8","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:23579614","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23579614","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 computer-aided molecular design","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.44999998807907104}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":77,"referenced_works":["https://openalex.org/W141181845","https://openalex.org/W1555648817","https://openalex.org/W1559298968","https://openalex.org/W1560473575","https://openalex.org/W1596348044","https://openalex.org/W1966041739","https://openalex.org/W1967964561","https://openalex.org/W1970658820","https://openalex.org/W1971652848","https://openalex.org/W1971808377","https://openalex.org/W1974422922","https://openalex.org/W1974734322","https://openalex.org/W1975570414","https://openalex.org/W1975691556","https://openalex.org/W1976975058","https://openalex.org/W1982842980","https://openalex.org/W1985588649","https://openalex.org/W1986165628","https://openalex.org/W1986240377","https://openalex.org/W1991483463","https://openalex.org/W1999519914","https://openalex.org/W2000579654","https://openalex.org/W2003486716","https://openalex.org/W2005445463","https://openalex.org/W2009423060","https://openalex.org/W2013760445","https://openalex.org/W2015848270","https://openalex.org/W2015907087","https://openalex.org/W2020040806","https://openalex.org/W2021832765","https://openalex.org/W2027423337","https://openalex.org/W2031793626","https://openalex.org/W2035292911","https://openalex.org/W2037633994","https://openalex.org/W2040496005","https://openalex.org/W2041189078","https://openalex.org/W2041203323","https://openalex.org/W2042110087","https://openalex.org/W2048199794","https://openalex.org/W2050066772","https://openalex.org/W2050456292","https://openalex.org/W2052030759","https://openalex.org/W2054881399","https://openalex.org/W2057846043","https://openalex.org/W2062378498","https://openalex.org/W2063535987","https://openalex.org/W2067416286","https://openalex.org/W2067455153","https://openalex.org/W2068350287","https://openalex.org/W2072569763","https://openalex.org/W2078653892","https://openalex.org/W2080156380","https://openalex.org/W2080961736","https://openalex.org/W2081719547","https://openalex.org/W2086190523","https://openalex.org/W2089887872","https://openalex.org/W2090786343","https://openalex.org/W2093426296","https://openalex.org/W2095501702","https://openalex.org/W2102377211","https://openalex.org/W2106810308","https://openalex.org/W2107506448","https://openalex.org/W2114819818","https://openalex.org/W2115318272","https://openalex.org/W2121895929","https://openalex.org/W2125792789","https://openalex.org/W2127760066","https://openalex.org/W2130479394","https://openalex.org/W2131366727","https://openalex.org/W2133641393","https://openalex.org/W2133773344","https://openalex.org/W2138866442","https://openalex.org/W2146041471","https://openalex.org/W2158534713","https://openalex.org/W2171068265","https://openalex.org/W2208175234","https://openalex.org/W2334089285"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4229748205","https://openalex.org/W2773493604","https://openalex.org/W2269591907","https://openalex.org/W2027065525","https://openalex.org/W2336040088"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":194},{"year":2025,"cited_by_count":784},{"year":2024,"cited_by_count":774},{"year":2023,"cited_by_count":792},{"year":2022,"cited_by_count":767},{"year":2021,"cited_by_count":687},{"year":2020,"cited_by_count":574},{"year":2019,"cited_by_count":390},{"year":2018,"cited_by_count":295},{"year":2017,"cited_by_count":240},{"year":2016,"cited_by_count":162},{"year":2015,"cited_by_count":121},{"year":2014,"cited_by_count":74},{"year":2013,"cited_by_count":26},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}
