{"id":"https://openalex.org/W2055817702","doi":"https://doi.org/10.1021/ci300430v","title":"Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data","display_name":"Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data","publication_year":2013,"publication_date":"2013-01-17","ids":{"openalex":"https://openalex.org/W2055817702","doi":"https://doi.org/10.1021/ci300430v","mag":"2055817702","pmid":"https://pubmed.ncbi.nlm.nih.gov/23327200"},"language":"en","primary_location":{"id":"doi:10.1021/ci300430v","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci300430v","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/A5085500481","display_name":"Katrina W. Lexa","orcid":"https://orcid.org/0000-0001-7163-2302"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katrina W. Lexa","raw_affiliation_strings":["Department of Medicinal\rChemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor,\rMichigan 48109-1065, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicinal\rChemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor,\rMichigan 48109-1065, United States","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074146124","display_name":"Heather A. Carlson","orcid":"https://orcid.org/0000-0002-7495-1699"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Heather A. Carlson","raw_affiliation_strings":["Department of Medicinal\rChemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor,\rMichigan 48109-1065, United States","Department of Medicinal#R#Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor,#R#Michigan 48109-1065, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicinal\rChemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor,\rMichigan 48109-1065, United States","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Medicinal#R#Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor,#R#Michigan 48109-1065, United States","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074146124"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":null,"apc_paid":null,"fwci":2.3939,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.88843558,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"53","issue":"2","first_page":"391","last_page":"402"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9998000264167786,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/extrapolation","display_name":"Extrapolation","score":0.7238553762435913},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5674511790275574},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.5644161701202393},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.529630720615387},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.49365362524986267},{"id":"https://openalex.org/keywords/complement","display_name":"Complement (music)","score":0.44594091176986694},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.43531864881515503},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.43076157569885254},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4044187664985657},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36150652170181274},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3096157908439636},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.23146593570709229},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19030678272247314},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15879109501838684}],"concepts":[{"id":"https://openalex.org/C132459708","wikidata":"https://www.wikidata.org/wiki/Q744069","display_name":"Extrapolation","level":2,"score":0.7238553762435913},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5674511790275574},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5644161701202393},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.529630720615387},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.49365362524986267},{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.44594091176986694},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.43531864881515503},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.43076157569885254},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4044187664985657},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36150652170181274},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3096157908439636},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.23146593570709229},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19030678272247314},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15879109501838684},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C188082640","wikidata":"https://www.wikidata.org/wiki/Q1780899","display_name":"Complementation","level":4,"score":0.0},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci300430v","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci300430v","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:23327200","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23327200","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},{"id":"pmh:oai:europepmc.org:2913296","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3581705","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1972091733","https://openalex.org/W1975503494","https://openalex.org/W1975688006","https://openalex.org/W1976499671","https://openalex.org/W1985494181","https://openalex.org/W1994923840","https://openalex.org/W1995206879","https://openalex.org/W1996989886","https://openalex.org/W1997036507","https://openalex.org/W2004709088","https://openalex.org/W2007112624","https://openalex.org/W2019048640","https://openalex.org/W2025157967","https://openalex.org/W2046813714","https://openalex.org/W2051381895","https://openalex.org/W2051710717","https://openalex.org/W2053871336","https://openalex.org/W2058527555","https://openalex.org/W2064514012","https://openalex.org/W2065856326","https://openalex.org/W2067174909","https://openalex.org/W2078823941","https://openalex.org/W2080653934","https://openalex.org/W2106140689","https://openalex.org/W2108921801","https://openalex.org/W2111108708","https://openalex.org/W2116211618","https://openalex.org/W2122339645","https://openalex.org/W2124026197","https://openalex.org/W2130479394","https://openalex.org/W2131639373","https://openalex.org/W2132629607","https://openalex.org/W2144288821","https://openalex.org/W2147066734","https://openalex.org/W2148455294","https://openalex.org/W2150360629","https://openalex.org/W2151884301","https://openalex.org/W2156059770","https://openalex.org/W2168865322"],"related_works":["https://openalex.org/W1968270095","https://openalex.org/W2220129715","https://openalex.org/W4296478327","https://openalex.org/W2042397106","https://openalex.org/W4361730764","https://openalex.org/W1965029248","https://openalex.org/W2333625343","https://openalex.org/W1960072520","https://openalex.org/W2023776155","https://openalex.org/W2387596242"],"abstract_inverted_index":{"Computational":[0],"approaches":[1],"to":[2,37,41,81,96,142,156,216],"fragment-based":[3],"drug":[4],"design":[5],"(FBDD)":[6],"can":[7,74],"complement":[8],"experiments":[9],"and":[10,131,171,209],"facilitate":[11],"the":[12,19,23,35,50,55,60,84,92,109,124,133,140,161,218,225],"identification":[13,219],"of":[14,25,86,94,126,139,173,192,220,227],"potential":[15],"hot":[16,87],"spots":[17,88],"along":[18],"protein":[20],"surface.":[21],"However,":[22],"evaluation":[24],"computational":[26],"methods":[27],"for":[28,112,137,153,165],"mapping":[29],"binding":[30],"sites":[31],"frequently":[32],"focuses":[33],"upon":[34,68],"ability":[36],"reproduce":[38],"crystallographic":[39,97,231],"coordinates":[40],"within":[42],"a":[43,76,181,189,213],"low":[44],"RMSD":[45],"threshold.":[46],"This":[47,73],"dependency":[48],"on":[49,123,129,168],"deposited":[51],"coordinate":[52],"data":[53,202],"overlooks":[54],"original":[56],"electron":[57],"density":[58,210],"from":[59],"experiment,":[61],"thus":[62],"techniques":[63],"may":[64,211],"be":[65,212],"developed":[66],"based":[67,167],"subjective-or":[69],"even":[70],"erroneous-atomic":[71],"coordinates.":[72],"become":[75],"significant":[77],"drawback":[78],"in":[79],"applications":[80],"systems":[82,143],"where":[83],"location":[85],"is":[89],"unknown.":[90],"On":[91],"basis":[93],"comparison":[95],"density,":[98],"we":[99,121],"previously":[100],"showed":[101],"that":[102,205],"mixed-solvent":[103],"molecular":[104],"dynamics":[105],"(MixMD)":[106],"accurately":[107],"identifies":[108],"active":[110],"site":[111],"HEWL,":[113],"with":[114,198],"acetonitrile":[115],"as":[116],"an":[117,150],"organic":[118],"solvent.":[119],"Here,":[120],"concentrated":[122],"influence":[125],"protic":[127],"solvent":[128,230],"simulation":[130,169],"refined":[132],"optimal":[134],"MixMD":[135,180,199],"approach":[136,152],"extrapolation":[138],"method":[141,183],"without":[144],"established":[145],"sites.":[146],"Our":[147],"results":[148,197],"establish":[149],"accurate":[151],"comparing":[154],"simulations":[155,208],"experiment.":[157],"We":[158],"have":[159],"outlined":[160,177],"most":[162],"efficient":[163],"strategy":[164],"MixMD,":[166],"length":[170],"number":[172],"runs.":[174],"The":[175],"development":[176],"here":[178],"makes":[179],"robust":[182],"which":[184],"should":[185],"prove":[186],"useful":[187,214],"across":[188],"broad":[190],"range":[191],"target":[193],"structures.":[194,232],"Lastly,":[195],"our":[196],"match":[200],"experimental":[201],"so":[203],"well":[204],"consistency":[206],"between":[207],"way":[215],"aid":[217],"probes":[221],"vs":[222],"waters":[223],"during":[224],"refinement":[226],"future":[228],"multiple":[229]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
