{"id":"https://openalex.org/W2530722635","doi":"https://doi.org/10.1007/s00894-016-3119-5","title":"A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1","display_name":"A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1","publication_year":2016,"publication_date":"2016-10-06","ids":{"openalex":"https://openalex.org/W2530722635","doi":"https://doi.org/10.1007/s00894-016-3119-5","mag":"2530722635","pmid":"https://pubmed.ncbi.nlm.nih.gov/27714533","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5054044"},"language":"en","primary_location":{"id":"doi:10.1007/s00894-016-3119-5","doi":"https://doi.org/10.1007/s00894-016-3119-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00894-016-3119-5","pdf_url":"https://link.springer.com/content/pdf/10.1007%2Fs00894-016-3119-5.pdf","source":{"id":"https://openalex.org/S113170167","display_name":"Journal of Molecular Modeling","issn_l":"0948-5023","issn":["0948-5023","1610-2940"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-d","jufo-1","medline","norway-1","poland-40","russia-white-list-2"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Molecular Modeling","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007%2Fs00894-016-3119-5.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060242817","display_name":"James J. P. Stewart","orcid":"https://orcid.org/0000-0001-6280-8695","observed_orcids":["https://orcid.org/0000-0001-6280-8695"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"James J. P. Stewart","raw_affiliation_strings":["Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO, 80921, USA. MrMOPAC@OpenMOPAC.net","Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO, 80921, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO, 80921, USA. MrMOPAC@OpenMOPAC.net","institution_ids":[]},{"raw_affiliation_string":"Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO, 80921, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5060242817"],"corresponding_institution_ids":[],"apc_list":{"value":4290,"currency":"USD","value_usd":4290},"apc_paid":{"value":4290,"currency":"USD","value_usd":4290},"fwci":0.6133,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.72440854,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"22","issue":"11","first_page":"259","last_page":"259"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.6157000064849854,"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":0.6157000064849854,"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":0.23170000314712524,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.06319999694824219,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/mth1","display_name":"MTH1","score":0.9490000009536743},{"id":"https://openalex.org/keywords/ogg1","display_name":"OGG1","score":0.8209999799728394},{"id":"https://openalex.org/keywords/substrate-specificity","display_name":"substrate specificity","score":0.6370000243186951},{"id":"https://openalex.org/keywords/binding-energy","display_name":"binding energy","score":0.6309999823570251},{"id":"https://openalex.org/keywords/site-directed-mutagenesis","display_name":"site-directed mutagenesis","score":0.6850000023841858},{"id":"https://openalex.org/keywords/binding-mechanism","display_name":"binding mechanism","score":0.47200000286102295},{"id":"https://openalex.org/keywords/molecular-docking","display_name":"molecular docking","score":0.5049999952316284}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6810451745986938},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.587480902671814},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.560500979423523},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5238761305809021},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.493431955575943},{"id":"https://openalex.org/C2777289219","wikidata":"https://www.wikidata.org/wiki/Q7632154","display_name":"Substrate (aquarium)","level":2,"score":0.45852982997894287},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.4230264127254486},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3227813243865967},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.25245118141174316},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08068424463272095},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.06578731536865234},{"id":"https://openalex.org/C185544564","wikidata":"https://www.wikidata.org/wiki/Q81197","display_name":"Nuclear physics","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","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/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003848","descriptor_name":"Deoxyguanine Nucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010744","descriptor_name":"Phosphoric Monoester Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","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":true},{"descriptor_ui":"D045643","descriptor_name":"DNA Repair Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1007/s00894-016-3119-5","doi":"https://doi.org/10.1007/s00894-016-3119-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00894-016-3119-5","pdf_url":"https://link.springer.com/content/pdf/10.1007%2Fs00894-016-3119-5.pdf","source":{"id":"https://openalex.org/S113170167","display_name":"Journal of Molecular Modeling","issn_l":"0948-5023","issn":["0948-5023","1610-2940"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-d","jufo-1","medline","norway-1","poland-40","russia-white-list-2"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Molecular Modeling","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:4023960","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5054044","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,"listed_in":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5054044","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5054044","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Mol Model","raw_type":"Text"},{"id":"pmid:27714533","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27714533","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,"listed_in":[],"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 molecular modeling","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1007/s00894-016-3119-5","doi":"https://doi.org/10.1007/s00894-016-3119-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s00894-016-3119-5","pdf_url":"https://link.springer.com/content/pdf/10.1007%2Fs00894-016-3119-5.pdf","source":{"id":"https://openalex.org/S113170167","display_name":"Journal of Molecular Modeling","issn_l":"0948-5023","issn":["0948-5023","1610-2940"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-d","jufo-1","medline","norway-1","poland-40","russia-white-list-2"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Molecular Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3841424451","display_name":"Migrate enzyme modeling technology from development site to experimental research","funder_award_id":"R44GM108085","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2530722635.pdf","grobid_xml":"https://content.openalex.org/works/W2530722635.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1492893078","https://openalex.org/W1605578858","https://openalex.org/W1972558086","https://openalex.org/W1973644758","https://openalex.org/W1985588649","https://openalex.org/W1988437166","https://openalex.org/W2000144532","https://openalex.org/W2003675370","https://openalex.org/W2008558900","https://openalex.org/W2015964119","https://openalex.org/W2018120102","https://openalex.org/W2032084435","https://openalex.org/W2038135746","https://openalex.org/W2044445096","https://openalex.org/W2050456292","https://openalex.org/W2055563809","https://openalex.org/W2064142965","https://openalex.org/W2078786624","https://openalex.org/W2082702530","https://openalex.org/W2088162897","https://openalex.org/W2092157292","https://openalex.org/W2130479394","https://openalex.org/W2134967712","https://openalex.org/W2143981217","https://openalex.org/W2144757830","https://openalex.org/W2148415990","https://openalex.org/W2158360182","https://openalex.org/W2158955044","https://openalex.org/W2159712022","https://openalex.org/W2285349883","https://openalex.org/W2301773610","https://openalex.org/W2304050602","https://openalex.org/W2313176581","https://openalex.org/W2321812084","https://openalex.org/W2323519269","https://openalex.org/W2403926370","https://openalex.org/W2470378089"],"related_works":["https://openalex.org/W2470378089","https://openalex.org/W2134667409","https://openalex.org/W7146083410","https://openalex.org/W2745469089","https://openalex.org/W2092946812","https://openalex.org/W2611525498","https://openalex.org/W2049462752","https://openalex.org/W1977330100","https://openalex.org/W2124602867","https://openalex.org/W2070775132"],"abstract_inverted_index":{"A":[0],"new":[1],"method":[2,170],"for":[3,28,151,225],"predicting":[4],"the":[5,24,44,52,54,57,81,92,109,118,138,142,146,154,159,168,173,179,184,188,196,219],"energy":[6,134,186],"contributions":[7,177],"to":[8,12,31,37,40,51,70,80,114,120,125,182],"substrate":[9],"binding":[10,93,143,185,220],"and":[11,94,145,148,158,187],"specificity":[13,189],"has":[14],"been":[15],"developed.":[16],"Conventional":[17],"global":[18],"optimization":[19],"methods":[20],"do":[21],"not":[22],"permit":[23],"subtle":[25],"effects":[26],"responsible":[27,150],"these":[29,164],"properties":[30],"be":[32,41,62,115],"modeled":[33,116],"with":[34,210],"sufficient":[35],"precision":[36],"allow":[38],"confidence":[39],"placed":[42],"in":[43,90,112,172,208],"results,":[45],"but":[46],"by":[47,194],"making":[48],"simple":[49],"alterations":[50],"model,":[53],"precisions":[55],"of":[56,133,163,178,190,198],"various":[58],"energies":[59],"involved":[60,111],"can":[61],"improved":[63],"from":[64,101],"about":[65],"\u00b12":[66],"kcal":[67,72],"mol":[68,73],"\u22121":[69,74],"\u00b10.1":[71],".":[75],"This":[76,213],"technique":[77,214],"was":[78],"applied":[79],"oxidized":[82,155],"nucleotide":[83,156],"pyrophosphohydrolase":[84],"enzyme":[85],"MTH1.":[86],"MTH1":[87,191],"is":[88],"unusual":[89],"that":[91,222],"reaction":[95,126],"sites":[96],"are":[97],"well":[98],"separated\u2014an":[99],"advantage":[100],"a":[102],"computational":[103],"chemistry":[104],"perspective,":[105],"as":[106],"it":[107],"allows":[108],"energetics":[110],"docking":[113],"without":[117],"need":[119],"consider":[121],"any":[122],"issues":[123],"relating":[124],"mechanisms.":[127],"In":[128],"this":[129],"study,":[130],"two":[131],"types":[132],"terms":[135],"were":[136,165,192,202,207],"investigated:":[137],"noncovalent":[139],"interactions":[140],"between":[141,153,227],"site":[144],"substrate,":[147],"those":[149],"discriminating":[152,226],"8-oxo-dGTP":[157],"normal":[160],"dGTP.":[161],"Both":[162],"investigated":[166],"using":[167],"semiempirical":[169],"PM7":[171],"program":[174],"MOPAC.":[175],"The":[176],"individual":[180],"residues":[181],"both":[183],"calculated":[193,205],"simulating":[195],"effect":[197],"mutations.":[199],"Where":[200],"comparisons":[201],"possible,":[203],"all":[204],"results":[206],"agreement":[209],"experimental":[211],"observations.":[212],"provides":[215],"fresh":[216],"insight":[217],"into":[218],"mechanism":[221],"enzymes":[223],"use":[224],"possible":[228],"substrates.":[229]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2017,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-10-21T00:00:00"}