{"id":"https://openalex.org/W1998568556","doi":"https://doi.org/10.1021/ci200274q","title":"<i>DSX</i>: A Knowledge-Based Scoring Function for the Assessment of Protein\u2013Ligand Complexes","display_name":"<i>DSX</i>: A Knowledge-Based Scoring Function for the Assessment of Protein\u2013Ligand Complexes","publication_year":2011,"publication_date":"2011-08-24","ids":{"openalex":"https://openalex.org/W1998568556","doi":"https://doi.org/10.1021/ci200274q","mag":"1998568556","pmid":"https://pubmed.ncbi.nlm.nih.gov/21863864"},"language":"en","primary_location":{"id":"doi:10.1021/ci200274q","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200274q","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/A5073990551","display_name":"Gerd Neudert","orcid":null},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Gerd Neudert","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, Philipps-Universit\u00e4t Marburg, Marbacher Weg 6, D-35032, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, Philipps-Universit\u00e4t Marburg, Marbacher Weg 6, D-35032, Germany","institution_ids":["https://openalex.org/I161103922"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005420915","display_name":"G. Klebe","orcid":"https://orcid.org/0000-0002-4913-390X"},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Gerhard Klebe","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, Philipps-Universit\u00e4t Marburg, Marbacher Weg 6, D-35032, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, Philipps-Universit\u00e4t Marburg, Marbacher Weg 6, D-35032, Germany","institution_ids":["https://openalex.org/I161103922"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5073990551"],"corresponding_institution_ids":["https://openalex.org/I161103922"],"apc_list":null,"apc_paid":null,"fwci":16.8025,"has_fulltext":false,"cited_by_count":264,"citation_normalized_percentile":{"value":0.99593972,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"51","issue":"10","first_page":"2731","last_page":"2745"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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":0.9979000091552734,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9894000291824341,"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/computer-science","display_name":"Computer science","score":0.6486135125160217},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"Dihedral angle","score":0.5959746241569519},{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.5771888494491577},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5217012763023376},{"id":"https://openalex.org/keywords/formalism","display_name":"Formalism (music)","score":0.4785621464252472},{"id":"https://openalex.org/keywords/atom","display_name":"Atom (system on chip)","score":0.44596895575523376},{"id":"https://openalex.org/keywords/torsion","display_name":"Torsion (gastropod)","score":0.4400278925895691},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3527165651321411},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3312807083129883},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.24984902143478394},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.21910226345062256},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14947912096977234},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.13200342655181885},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.10739201307296753},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.10421115159988403},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.08362483978271484}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6486135125160217},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.5959746241569519},{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.5771888494491577},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5217012763023376},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.4785621464252472},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.44596895575523376},{"id":"https://openalex.org/C77461463","wikidata":"https://www.wikidata.org/wiki/Q7827201","display_name":"Torsion (gastropod)","level":2,"score":0.4400278925895691},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3527165651321411},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3312807083129883},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.24984902143478394},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.21910226345062256},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14947912096977234},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.13200342655181885},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.10739201307296753},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.10421115159988403},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.08362483978271484},{"id":"https://openalex.org/C558565934","wikidata":"https://www.wikidata.org/wiki/Q2743","display_name":"Musical","level":2,"score":0.0},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","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},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D008958","descriptor_name":"Models, Molecular","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":"D008958","descriptor_name":"Models, Molecular","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":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","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":"D013816","descriptor_name":"Thermodynamics","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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci200274q","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200274q","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:21863864","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21863864","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":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1505394602","https://openalex.org/W1549357029","https://openalex.org/W1589812083","https://openalex.org/W1592950931","https://openalex.org/W1596574470","https://openalex.org/W1605578858","https://openalex.org/W1656114533","https://openalex.org/W1970658820","https://openalex.org/W1973191530","https://openalex.org/W1974809008","https://openalex.org/W1974885083","https://openalex.org/W1975222610","https://openalex.org/W1975948225","https://openalex.org/W1984021058","https://openalex.org/W1985588649","https://openalex.org/W1988111902","https://openalex.org/W1992583240","https://openalex.org/W1993046136","https://openalex.org/W1993403967","https://openalex.org/W2001956250","https://openalex.org/W2002733813","https://openalex.org/W2003356525","https://openalex.org/W2012084558","https://openalex.org/W2014704001","https://openalex.org/W2017702218","https://openalex.org/W2032842297","https://openalex.org/W2042001675","https://openalex.org/W2043429268","https://openalex.org/W2047544230","https://openalex.org/W2050456292","https://openalex.org/W2051163038","https://openalex.org/W2053503396","https://openalex.org/W2061079400","https://openalex.org/W2066787645","https://openalex.org/W2073425942","https://openalex.org/W2076290992","https://openalex.org/W2082296224","https://openalex.org/W2085315829","https://openalex.org/W2090847673","https://openalex.org/W2092285329","https://openalex.org/W2096360825","https://openalex.org/W2098312592","https://openalex.org/W2100094261","https://openalex.org/W2102377211","https://openalex.org/W2105527266","https://openalex.org/W2107506448","https://openalex.org/W2111796195","https://openalex.org/W2114779636","https://openalex.org/W2117197915","https://openalex.org/W2118587156","https://openalex.org/W2120898782","https://openalex.org/W2121895929","https://openalex.org/W2128332459","https://openalex.org/W2158360182","https://openalex.org/W2158534713","https://openalex.org/W2159006106","https://openalex.org/W2169562071","https://openalex.org/W2411981780","https://openalex.org/W4322696300"],"related_works":["https://openalex.org/W2058674645","https://openalex.org/W1594539819","https://openalex.org/W2766845742","https://openalex.org/W2007257620","https://openalex.org/W4213038553","https://openalex.org/W2130867670","https://openalex.org/W1984029386","https://openalex.org/W4312202637","https://openalex.org/W2136513242","https://openalex.org/W2336040088"],"abstract_inverted_index":{"We":[0],"introduce":[1],"the":[2,31,59,104,127,168],"new":[3],"knowledge-based":[4],"scoring":[5,109],"function":[6],"DSX":[7,25,112,138],"that":[8],"consists":[9],"of":[10,34,43,84,106,144,150],"distance-dependent":[11],"pair":[12,26,79],"potentials,":[13,17],"novel":[14],"torsion":[15,131],"angle":[16],"and":[18,71,120,123,133,142,171],"newly":[19],"defined":[20],"solvent":[21],"accessible":[22],"surface-dependent":[23],"potentials.":[24],"potentials":[27,80,135],"are":[28],"based":[29,91],"on":[30,92],"statistical":[32],"formalism":[33],"DrugScore,":[35],"extended":[36],"by":[37],"a":[38,93],"much":[39],"more":[40],"specialized":[41],"set":[42,97],"atom":[44,61,85],"types.":[45,62],"The":[46,162],"original":[47],"DrugScore-like":[48],"reference":[49],"state":[50],"is":[51,87,98,136,139,164],"rather":[52],"unstable":[53],"with":[54,116,130,147],"respect":[55,117],"to":[56,67,72,103,118,167],"modifications":[57],"in":[58,158],"used":[60],"Therefore,":[63],"an":[64],"important":[65],"method":[66],"overcome":[68],"this":[69],"problem":[70],"allow":[73],"for":[74,81],"robust":[75],"results":[76],"when":[77],"deriving":[78],"arbitrary":[82],"sets":[83],"types":[86],"presented.":[88],"A":[89],"validation":[90],"carefully":[94],"prepared":[95],"test":[96],"shown,":[99],"enabling":[100],"direct":[101],"comparison":[102],"majority":[105],"other":[107],"popular":[108,151],"functions.":[110],"Here,":[111],"features":[113,149],"superior":[114],"performance":[115],"docking-":[119],"ranking":[121],"power":[122],"runtime":[124],"requirements.":[125],"Furthermore,":[126],"beneficial":[128],"combination":[129],"angle-dependent":[132],"desolvation-dependent":[134],"demonstrated.":[137],"robust,":[140],"flexible,":[141],"capable":[143],"working":[145],"together":[146],"special":[148],"docking":[152],"engines,":[153],"e.g.,":[154],"flexible":[155],"protein":[156],"residues":[157],"AutoDock":[159],"or":[160],"GOLD.":[161],"program":[163],"freely":[165],"available":[166],"scientific":[169],"community":[170],"can":[172],"be":[173],"downloaded":[174],"from":[175],"our":[176],"Web":[177],"site":[178],"www.agklebe.de":[179],".":[180]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":29},{"year":2020,"cited_by_count":31},{"year":2019,"cited_by_count":20},{"year":2018,"cited_by_count":23},{"year":2017,"cited_by_count":19},{"year":2016,"cited_by_count":20},{"year":2015,"cited_by_count":16},{"year":2014,"cited_by_count":26},{"year":2013,"cited_by_count":15},{"year":2012,"cited_by_count":10}],"updated_date":"2026-04-06T07:47:59.780226","created_date":"2016-06-24T00:00:00"}