{"id":"https://openalex.org/W1976044546","doi":"https://doi.org/10.1145/2016741.2016746","title":"Towards high-throughput, high-performance computational estimation of binding affinities for patient specific HIV-1 protease sequences","display_name":"Towards high-throughput, high-performance computational estimation of binding affinities for patient specific HIV-1 protease sequences","publication_year":2011,"publication_date":"2011-07-18","ids":{"openalex":"https://openalex.org/W1976044546","doi":"https://doi.org/10.1145/2016741.2016746","mag":"1976044546"},"language":"en","primary_location":{"id":"doi:10.1145/2016741.2016746","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2016741.2016746","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5028019560","display_name":"Owain Kenway","orcid":null},"institutions":[{"id":"https://openalex.org/I4210115172","display_name":"Oxford Centre for Computational Neuroscience","ror":"https://ror.org/026ejyb70","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I4210115172"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Owain Kenway","raw_affiliation_strings":["Center for Computational Science, UCL, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Science, UCL, London, UK","institution_ids":["https://openalex.org/I4210115172","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066932343","display_name":"David W. Wright","orcid":"https://orcid.org/0000-0002-5124-8044"},"institutions":[{"id":"https://openalex.org/I4210115172","display_name":"Oxford Centre for Computational Neuroscience","ror":"https://ror.org/026ejyb70","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I4210115172"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David W. Wright","raw_affiliation_strings":["Center for Computational Science, UCL, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Science, UCL, London, UK","institution_ids":["https://openalex.org/I4210115172","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005705490","display_name":"Helmut Heller","orcid":null},"institutions":[{"id":"https://openalex.org/I4210163716","display_name":"Leibniz Supercomputing Centre","ror":"https://ror.org/05558nw16","country_code":"DE","type":"facility","lineage":["https://openalex.org/I109144446","https://openalex.org/I4210163716"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Helmut Heller","raw_affiliation_strings":["Leibniz Supercomputing, Centre Garching, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Leibniz Supercomputing, Centre Garching, Germany","institution_ids":["https://openalex.org/I4210163716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057270628","display_name":"Andr\u00e9 Merzky","orcid":"https://orcid.org/0000-0002-7228-4327"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andre Merzky","raw_affiliation_strings":["CCT, Louisiana State University, Baton Rouge, LA","CCT, Louisiana State University, Baton Rouge, LA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CCT, Louisiana State University, Baton Rouge, LA","institution_ids":["https://openalex.org/I121820613"]},{"raw_affiliation_string":"CCT, Louisiana State University, Baton Rouge, LA#TAB#","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022859505","display_name":"Gavin J. Pringle","orcid":"https://orcid.org/0000-0002-5026-4093"},"institutions":[{"id":"https://openalex.org/I45442566","display_name":"El Paso Community College","ror":"https://ror.org/01gswfc04","country_code":"US","type":"education","lineage":["https://openalex.org/I45442566"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gavin Pringle","raw_affiliation_strings":["EPCC, Edinburgh, Edinburgh UK","EPCC, Edinburgh, Edinburgh UK#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EPCC, Edinburgh, Edinburgh UK","institution_ids":[]},{"raw_affiliation_string":"EPCC, Edinburgh, Edinburgh UK#TAB#","institution_ids":["https://openalex.org/I45442566"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072699196","display_name":"Jules Wolfrat","orcid":"https://orcid.org/0000-0002-1121-2864"},"institutions":[{"id":"https://openalex.org/I4210108155","display_name":"SURFsara (Netherlands)","ror":"https://ror.org/01k0v6g02","country_code":"NL","type":"company","lineage":["https://openalex.org/I4210108155"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jules Wolfrat","raw_affiliation_strings":["SARA Computing &amp; Networking Services, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SARA Computing &amp; Networking Services, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I4210108155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066453821","display_name":"Peter V. Coveney","orcid":"https://orcid.org/0000-0002-8787-7256"},"institutions":[{"id":"https://openalex.org/I4210115172","display_name":"Oxford Centre for Computational Neuroscience","ror":"https://ror.org/026ejyb70","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I4210115172"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Peter Coveney","raw_affiliation_strings":["Center for Computational Science, UCL London, UK","Center for Computational Science, UCL, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Science, UCL London, UK","institution_ids":["https://openalex.org/I4210115172","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Center for Computational Science, UCL, London, UK","institution_ids":["https://openalex.org/I4210115172","https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038763846","display_name":"Shantenu Jha","orcid":"https://orcid.org/0000-0002-5040-026X"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shantenu Jha","raw_affiliation_strings":["Rutgers University, NJ &amp; Louisiana State University, Baton Rouge LA","Rutgers University, NJ & Louisiana State University, Baton Rouge LA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rutgers University, NJ &amp; Louisiana State University, Baton Rouge LA","institution_ids":["https://openalex.org/I121820613","https://openalex.org/I102322142"]},{"raw_affiliation_string":"Rutgers University, NJ & Louisiana State University, Baton Rouge LA#TAB#","institution_ids":["https://openalex.org/I121820613"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06614265,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"62","issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9815999865531921,"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":0.9815999865531921,"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/T10112","display_name":"HIV Research and Treatment","score":0.977400004863739,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9718999862670898,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/computer-science","display_name":"Computer science","score":0.5890592932701111},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.560904324054718},{"id":"https://openalex.org/keywords/epistasis","display_name":"Epistasis","score":0.5394741892814636},{"id":"https://openalex.org/keywords/binding-affinities","display_name":"Binding affinities","score":0.5175439715385437},{"id":"https://openalex.org/keywords/informatics","display_name":"Informatics","score":0.5142399668693542},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.4807003140449524},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4193105101585388},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.41069328784942627},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29483044147491455},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2783575654029846},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.15020841360092163},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12235870957374573}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5890592932701111},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.560904324054718},{"id":"https://openalex.org/C61727976","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Epistasis","level":3,"score":0.5394741892814636},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.5175439715385437},{"id":"https://openalex.org/C191630685","wikidata":"https://www.wikidata.org/wiki/Q4027615","display_name":"Informatics","level":2,"score":0.5142399668693542},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.4807003140449524},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4193105101585388},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.41069328784942627},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29483044147491455},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2783575654029846},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.15020841360092163},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12235870957374573},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","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},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2016741.2016746","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2016741.2016746","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery","raw_type":"proceedings-article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:10035001","is_oa":false,"landing_page_url":"http://discovery.ucl.ac.uk/10035001/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"     In:       (2011)     ","raw_type":"Proceedings paper"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.5799999833106995,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2750898892","display_name":null,"funder_award_id":"GR/D0766171/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5558169809","display_name":null,"funder_award_id":"NSF-OCI 0710874","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320337377","display_name":"Office of Advanced Cyberinfrastructure","ror":"https://ror.org/04nh1dc89"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W152428861","https://openalex.org/W1965411625","https://openalex.org/W1966509953","https://openalex.org/W1966720984","https://openalex.org/W1975580333","https://openalex.org/W1987809254","https://openalex.org/W1988562891","https://openalex.org/W1998645872","https://openalex.org/W2009467617","https://openalex.org/W2028835439","https://openalex.org/W2039353947","https://openalex.org/W2054931962","https://openalex.org/W2058616175","https://openalex.org/W2062506290","https://openalex.org/W2069123478","https://openalex.org/W2084550263","https://openalex.org/W2097636949","https://openalex.org/W2099340616","https://openalex.org/W2100445717","https://openalex.org/W2113020311","https://openalex.org/W2113264508","https://openalex.org/W2117620409","https://openalex.org/W2118233996","https://openalex.org/W2126428030","https://openalex.org/W2139880162","https://openalex.org/W2147993766","https://openalex.org/W2150981663"],"related_works":["https://openalex.org/W3187200704","https://openalex.org/W2031259671","https://openalex.org/W3112966125","https://openalex.org/W2108080735","https://openalex.org/W1990832091","https://openalex.org/W2095596733","https://openalex.org/W4240532245","https://openalex.org/W1961356786","https://openalex.org/W1966443150","https://openalex.org/W4248477353"],"abstract_inverted_index":{"The":[0,96,116],"rapid":[1],"acquisition":[2],"of":[3,14,37,57,67,93,98,149,151,168,171,183,213,225,236,245,249,259,271],"mutations":[4,26,58],"conferring":[5],"resistance":[6,22,35,69,150],"to":[7,24,32,82,135,155,194,202,209,279],"particular":[8,153],"drugs":[9],"remains":[10],"a":[11,131,152,174],"significant":[12],"cause":[13],"anti-HIV":[15],"treatment":[16],"failure.":[17],"Informatics":[18],"based":[19,185],"techniques":[20],"give":[21],"scores":[23],"individual":[25,273],"which":[27,78,127],"can":[28,102,253],"be":[29,103,156],"combined":[30],"additively":[31],"assess":[33],"the":[34,45,65,80,91,106,112,124,147,166,181,187,227,233,237,246,256,272,280,284],"levels":[36],"complete":[38],"sequences.":[39],"It":[40],"is":[41,48,74,123,162,173],"likely":[42],"however,":[43],"that":[44,252],"full":[46],"picture":[47],"more":[49,266],"complicated,":[50],"with":[51,111,231],"non-linear":[52],"epistatic":[53],"effects":[54],"between":[55],"combinations":[56],"playing":[59],"an":[60,160],"important":[61],"role":[62],"in":[63,229,289,302],"determining":[64],"level":[66,148],"viral":[68],"[1,":[70],"2].":[71],"Molecular":[72],"dynamics":[73,97],"one":[75,244],"simulation":[76],"technique":[77],"offers":[79],"ability":[81],"derive":[83],"quantitative":[84],"(as":[85],"well":[86],"as":[87,207],"qualitative)":[88],"insight":[89],"into":[90],"interplay":[92],"resistance-causing":[94],"mutations.":[95],"sequence":[99,154],"specific":[100],"models":[101],"simulated":[104],"and":[105,143,165,223,295,298],"free":[107,117],"energy":[108,118],"change":[109,119],"associated":[110],"drug":[113,132],"binding":[114,121],"calculated.":[115],"(or":[120],"affinity)":[122],"thermodynamic":[125],"quantity":[126],"determines":[128],"how":[129],"tightly":[130],"will":[133],"bind":[134],"its":[136],"target.":[137],"Hence,":[138],"comparing":[139],"values":[140],"for":[141,190,215,286],"mutant":[142],"wildtype":[144],"systems":[145],"allows":[146,200],"estimated.":[157],"Validating":[158],"such":[159,206],"approach":[161],"computationally":[163],"demanding":[164],"management":[167],"large":[169],"numbers":[170],"simulations":[172],"considerable":[175],"administrative":[176],"challenge.":[177],"Here":[178],"we":[179],"present":[180],"use":[182],"tools":[184],"on":[186],"Simple":[188],"API":[189],"Grid":[191],"Applications":[192],"(SAGA)":[193],"tackle":[195],"this":[196,290,303],"computational":[197,250,257,267],"problem.":[198],"This":[199,218],"us":[201],"utilise":[203],"high-end":[204],"infrastructure,":[205],"TeraGrid/XD,":[208],"provide":[210],"extreme":[211],"scales":[212],"throughput":[214],"highperformance":[216],"simulations.":[217],"paper":[219],"presents":[220],"initial":[221],"results":[222],"experience":[224],"using":[226],"TeraGrid":[228],"conjunction":[230],"DEISA,":[232],"European":[234],"analogue":[235],"US":[238],"TeraGrid.":[239],"High-throughput":[240],"(high-performance)":[241],"calculations":[242],"are":[243],"few":[247],"classes":[248],"problems":[251],"easily":[254],"exploit":[255],"power":[258,268],"widely":[260],"distributed":[261],"computing":[262],"resources,":[263],"thereby":[264],"amassing":[265],"than":[269],"any":[270],"resources":[274],"could":[275],"offer.":[276],"In":[277],"addition":[278],"resource":[281],"utilization":[282],"rationale":[283],"need":[285],"cross-Grid":[287],"capabilities":[288],"case":[291],"arises":[292],"from":[293],"shared":[294],"complementary":[296],"scientific":[297],"technical":[299],"skills":[300],"found":[301],"intercontinental":[304],"collaboration.":[305]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
