{"id":"https://openalex.org/W646505649","doi":null,"title":"Predicting the location and binding affinity of small molecules in protein binding sites","display_name":"Predicting the location and binding affinity of small molecules in protein binding sites","publication_year":2012,"publication_date":"2012-09-30","ids":{"openalex":"https://openalex.org/W646505649","mag":"646505649"},"language":"en","primary_location":{"id":"pmh:oai:eprints.soton.ac.uk:348170","doi":null,"is_oa":true,"landing_page_url":"https://eprints.soton.ac.uk/id/eprint/348170/1/_soton.ac.uk_ude_PersonalFiles_Users_lp5_mydocuments_Theses_20PDF_20files_Thesis_MSBodnarchuk.pdf","pdf_url":"https://eprints.soton.ac.uk/348170/1/__soton.ac.uk_ude_PersonalFiles_Users_lp5_mydocuments_Theses%2520PDF%2520files_Thesis_MSBodnarchuk.pdf","source":{"id":"https://openalex.org/S4306401019","display_name":"ePrints Soton (University of Southampton)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I43439940","host_organization_name":"University of Southampton","host_organization_lineage":["https://openalex.org/I43439940"],"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":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://eprints.soton.ac.uk/348170/1/__soton.ac.uk_ude_PersonalFiles_Users_lp5_mydocuments_Theses%2520PDF%2520files_Thesis_MSBodnarchuk.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004157917","display_name":"Michael S. Bodnarchuk","orcid":"https://orcid.org/0000-0002-9172-1203","observed_orcids":["https://orcid.org/0000-0002-9172-1203"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Michael S. Bodnarchuk","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-9172-1203","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5004157917"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9833999872207642,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9833999872207642,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.008200000040233135,"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":0.002199999988079071,"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/protein-binding-sites","display_name":"protein binding sites","score":0.9369999766349792},{"id":"https://openalex.org/keywords/binding-affinity-prediction","display_name":"binding affinity prediction","score":0.8009999990463257},{"id":"https://openalex.org/keywords/hydration-sites","display_name":"hydration sites","score":0.7820000052452087},{"id":"https://openalex.org/keywords/grand-canonical-monte-carlo-simulation","display_name":"grand canonical Monte Carlo simulation","score":0.8999999761581421},{"id":"https://openalex.org/keywords/binding-free-energy","display_name":"binding free energy","score":0.8320000171661377},{"id":"https://openalex.org/keywords/fragment-based-drug-discovery","display_name":"fragment-based drug discovery","score":0.7929999828338623},{"id":"https://openalex.org/keywords/hydrophobic-cavity","display_name":"hydrophobic cavity","score":0.7639999985694885},{"id":"https://openalex.org/keywords/protein-kinases","display_name":"protein kinases","score":0.9509999752044678},{"id":"https://openalex.org/keywords/kinesin-spindle-protein","display_name":"kinesin spindle protein","score":0.8489999771118164},{"id":"https://openalex.org/keywords/factor-xa","display_name":"factor Xa","score":0.9919999837875366},{"id":"https://openalex.org/keywords/neuraminidase","display_name":"neuraminidase","score":0.8360000252723694},{"id":"https://openalex.org/keywords/ligand-design","display_name":"ligand design","score":0.890999972820282}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6001039147377014},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.5797083377838135},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5100646615028381},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.4625619649887085},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.4520612955093384},{"id":"https://openalex.org/C22499117","wikidata":"https://www.wikidata.org/wiki/Q2253702","display_name":"Interaction energy","level":3,"score":0.4387272000312805},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4376167058944702},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.42429226636886597},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.39335545897483826},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34551340341567993},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1504105031490326},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09477156400680542},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:eprints.soton.ac.uk:348170","doi":null,"is_oa":true,"landing_page_url":"https://eprints.soton.ac.uk/id/eprint/348170/1/_soton.ac.uk_ude_PersonalFiles_Users_lp5_mydocuments_Theses_20PDF_20files_Thesis_MSBodnarchuk.pdf","pdf_url":"https://eprints.soton.ac.uk/348170/1/__soton.ac.uk_ude_PersonalFiles_Users_lp5_mydocuments_Theses%2520PDF%2520files_Thesis_MSBodnarchuk.pdf","source":{"id":"https://openalex.org/S4306401019","display_name":"ePrints Soton (University of Southampton)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I43439940","host_organization_name":"University of Southampton","host_organization_lineage":["https://openalex.org/I43439940"],"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":"Thesis"},{"id":"mag:646505649","doi":null,"is_oa":false,"landing_page_url":"http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.568888","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:eprints.soton.ac.uk:348170","doi":null,"is_oa":true,"landing_page_url":"https://eprints.soton.ac.uk/id/eprint/348170/1/_soton.ac.uk_ude_PersonalFiles_Users_lp5_mydocuments_Theses_20PDF_20files_Thesis_MSBodnarchuk.pdf","pdf_url":"https://eprints.soton.ac.uk/348170/1/__soton.ac.uk_ude_PersonalFiles_Users_lp5_mydocuments_Theses%2520PDF%2520files_Thesis_MSBodnarchuk.pdf","source":{"id":"https://openalex.org/S4306401019","display_name":"ePrints Soton (University of Southampton)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I43439940","host_organization_name":"University of Southampton","host_organization_lineage":["https://openalex.org/I43439940"],"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":"Thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W646505649.pdf","grobid_xml":"https://content.openalex.org/works/W646505649.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2015647581","https://openalex.org/W2005647584","https://openalex.org/W4310784129","https://openalex.org/W1978809115","https://openalex.org/W7171403482","https://openalex.org/W3121804740","https://openalex.org/W2770483985","https://openalex.org/W2608872311","https://openalex.org/W2883886126","https://openalex.org/W569276333"],"abstract_inverted_index":{"In":[0],"this":[1,28],"thesis,":[2],"various":[3],"methods":[4,64,91,104,152,174],"for":[5,126,142],"locating":[6],"and":[7,15,40,71,86,165,194,250,262,265,280],"scoring":[8],"the":[9,45,69,90,93,103,106,112,127,131,143,151,173,187,220,258,268,275],"binding":[10,20,108,132,188],"affinity":[11,72],"of":[12,27,73,102,111,130,135,145,150,158,186,217,277],"water":[13,74,113,136,281],"molecules":[14,58,114,282],"molecular":[16,278],"fragments":[17,279],"in":[18,191,205],"protein":[19,166],"sites":[21],"are":[22,65,213],"described.":[23],"The":[24,118,148,210],"primary":[25],"aim":[26],"work":[29],"is":[30,231,255,270],"to":[31,37,52,67,92,115,123,178,201,215,219,272,284],"understand":[32],"how":[33,56,172,195],"different":[34,63],"methodologies":[35],"compare":[36],"one":[38],"another":[39],"how,":[41],"by":[42,242],"carefully":[43],"choosing":[44],"correct":[46],"method,":[47],"they":[48],"can":[49,97,175,198],"be":[50,98,124,176,199,216],"used":[51,66,154,177,200,256],"extract":[53],"information":[54],"on":[55,155],"small":[57],"interact":[59],"with":[60],"proteins.":[61],"Three":[62],"predict":[68,105,180],"location":[70],"molecules;":[75],"Just":[76],"Add":[77],"Water":[78],"Molecules":[79],"(JAWS),":[80],"Grand":[81],"Canonical":[82],"Monte":[83],"Carlo":[84],"(GCMC)":[85],"double-decoupling.":[87],"By":[88],"applying":[89],"N9-Neuraminidase":[94],"system,":[95],"it":[96],"shown":[99,122],"that":[100,267],"all":[101],"same":[107],"free":[109,133,189],"energy":[110,134,190],"within":[116],"error.":[117],"JAWS":[119,224],"method":[120,254,269],"was":[121,140],"advantageous":[125],"rapid":[128],"prediction":[129,144],"molecules,":[137],"whilst":[138],"GCMC":[139,192],"preferred":[141],"hydration":[146,181],"sites.":[147],"combination":[149],"were":[153],"a":[156,184,206],"variety":[157],"novel":[159],"test":[160,169],"cases,":[161],"including":[162],"hydrophobic":[163],"cavities":[164],"kinases.":[167],"These":[168],"cases":[170],"highlight":[171],"accurately":[179,273],"patterns":[182,197],"as":[183,247],"function":[185],"simulations,":[193],"these":[196],"dictate":[202],"ligand":[203],"design":[204],"drug":[207,228],"discovery":[208,229],"context.":[209],"approaches":[211,245],"described":[212],"likely":[214],"interest":[218],"pharmaceutical":[221],"industry.":[222],"A":[223],"based":[225,227],"fragment":[226,251],"methodology":[230],"also":[232],"described,":[233],"which":[234],"takes":[235],"into":[236],"account":[237],"key":[238],"features":[239],"commonly":[240],"neglected":[241],"existing":[243],"computational":[244],"such":[246],"fragment-solvent":[248],"competition":[249],"desolvation.":[252],"This":[253],"upon":[257],"Kinesin":[259],"Spindle":[260],"Protein":[261],"factor":[263],"Xa,":[264],"demonstrates":[266],"able":[271],"locate":[274],"position":[276],"compared":[283],"crystallographic":[285],"ligands.":[286]},"counts_by_year":[],"updated_date":"2026-10-27T15:51:10.671819","created_date":"2016-06-24T00:00:00"}