{"id":"https://openalex.org/W2107499603","doi":"https://doi.org/10.1093/bioinformatics/btt699","title":"GPU linear and non-linear Poisson\u2013Boltzmann solver module for DelPhi","display_name":"GPU linear and non-linear Poisson\u2013Boltzmann solver module for DelPhi","publication_year":2013,"publication_date":"2013-11-30","ids":{"openalex":"https://openalex.org/W2107499603","doi":"https://doi.org/10.1093/bioinformatics/btt699","mag":"2107499603","pmid":"https://pubmed.ncbi.nlm.nih.gov/24292939"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt699","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt699","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/4/569/48917335/bioinformatics_30_4_569.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/4/569/48917335/bioinformatics_30_4_569.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022887048","display_name":"Jos\u00e9 Colmenares","orcid":null},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Colmenares","raw_affiliation_strings":["1 Drug Discovery and Development Department and 2Advanced Robotics Department, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova - Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Drug Discovery and Development Department and 2Advanced Robotics Department, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova - Italy","institution_ids":["https://openalex.org/I30771326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025925261","display_name":"Jes\u00fas Ortiz","orcid":"https://orcid.org/0000-0001-9475-1945"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Jes\u00fas Ortiz","raw_affiliation_strings":["1 Drug Discovery and Development Department and 2Advanced Robotics Department, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova - Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Drug Discovery and Development Department and 2Advanced Robotics Department, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova - Italy","institution_ids":["https://openalex.org/I30771326"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089704088","display_name":"Walter Rocchia","orcid":"https://orcid.org/0000-0003-2480-7151"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Walter Rocchia","raw_affiliation_strings":["1 Drug Discovery and Development Department and 2Advanced Robotics Department, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova - Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Drug Discovery and Development Department and 2Advanced Robotics Department, Istituto Italiano di Tecnologia (IIT), via Morego, 30, 16163 Genova - Italy","institution_ids":["https://openalex.org/I30771326"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5089704088"],"corresponding_institution_ids":["https://openalex.org/I30771326"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.5557,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.67199595,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"30","issue":"4","first_page":"569","last_page":"570"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6539000272750854,"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":0.6539000272750854,"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/T11751","display_name":"Lattice Boltzmann Simulation Studies","score":0.12240000069141388,"subfield":{"id":"https://openalex.org/subfields/2206","display_name":"Computational Mechanics"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.02329999953508377,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.8179705142974854},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7692468166351318},{"id":"https://openalex.org/keywords/solver","display_name":"Solver","score":0.7359520196914673},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7012083530426025},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6229618787765503},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5979797840118408},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5115216970443726},{"id":"https://openalex.org/keywords/linear-system","display_name":"Linear system","score":0.47121351957321167},{"id":"https://openalex.org/keywords/delphi","display_name":"Delphi","score":0.4318233132362366},{"id":"https://openalex.org/keywords/linear-equation","display_name":"Linear equation","score":0.41036257147789},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.37231752276420593},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35399436950683594},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1755947768688202},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08942446112632751}],"concepts":[{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.8179705142974854},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7692468166351318},{"id":"https://openalex.org/C2778770139","wikidata":"https://www.wikidata.org/wiki/Q1966904","display_name":"Solver","level":2,"score":0.7359520196914673},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7012083530426025},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6229618787765503},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5979797840118408},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5115216970443726},{"id":"https://openalex.org/C6802819","wikidata":"https://www.wikidata.org/wiki/Q1072174","display_name":"Linear system","level":2,"score":0.47121351957321167},{"id":"https://openalex.org/C2779495148","wikidata":"https://www.wikidata.org/wiki/Q487378","display_name":"Delphi","level":2,"score":0.4318233132362366},{"id":"https://openalex.org/C77346573","wikidata":"https://www.wikidata.org/wiki/Q484637","display_name":"Linear equation","level":2,"score":0.41036257147789},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.37231752276420593},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35399436950683594},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1755947768688202},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08942446112632751},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"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":"D000099252","descriptor_name":"Fatty Acid Amide Hydrolases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000581","descriptor_name":"Amidohydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000581","descriptor_name":"Amidohydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000581","descriptor_name":"Amidohydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","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},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btt699","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt699","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/4/569/48917335/bioinformatics_30_4_569.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3928518","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3928518","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,"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":"Bioinformatics","raw_type":"Text"},{"id":"pmid:24292939","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24292939","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:www.research.unipd.it:11577/3105933","is_oa":false,"landing_page_url":"http://hdl.handle.net/11577/3105933","pdf_url":null,"source":{"id":"https://openalex.org/S4306402547","display_name":"Padua Research Archive (University of Padova)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt699","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt699","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/4/569/48917335/bioinformatics_30_4_569.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3233386537","display_name":null,"funder_award_id":"R01GM093937","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8023679455","display_name":"DelPhi:  Software for Electrostatic Modeling of Biomolecules and Objects","funder_award_id":"1r01gm093937-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2107499603.pdf","grobid_xml":"https://content.openalex.org/works/W2107499603.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2003761244","https://openalex.org/W2018375258","https://openalex.org/W2039665613","https://openalex.org/W2057664120","https://openalex.org/W2079802323","https://openalex.org/W2106115249","https://openalex.org/W2127116852","https://openalex.org/W2883176708","https://openalex.org/W4239957396","https://openalex.org/W4379033776","https://openalex.org/W6651517965"],"related_works":["https://openalex.org/W2983282793","https://openalex.org/W4309988886","https://openalex.org/W2962718424","https://openalex.org/W3008021696","https://openalex.org/W2500993308","https://openalex.org/W2751036783","https://openalex.org/W2613072034","https://openalex.org/W1441806976","https://openalex.org/W3195219148","https://openalex.org/W1999760939"],"abstract_inverted_index":{"SUMMARY:":[0],"In":[1],"this":[2],"work,":[3],"we":[4],"present":[5],"a":[6,11,69],"CUDA-based":[7],"GPU":[8,36],"implementation":[9,79],"of":[10,73,77,88],"Poisson-Boltzmann":[12],"equation":[13],"solver,":[14],"in":[15,54,94],"both":[16,93],"the":[17,35,44,55,78,95],"linear":[18,96],"and":[19,31,66,80,97,107],"non-linear":[20,98],"versions,":[21],"using":[22,64],"double":[23],"precision.":[24],"A":[25,86],"finite":[26],"difference":[27],"scheme":[28],"is":[29,51,105],"adopted":[30],"made":[32],"suitable":[33],"for":[34,47],"architecture.":[37],"The":[38,59,103],"resulting":[39],"code":[40],"was":[41,91],"interfaced":[42],"with":[43],"electrostatics":[45],"software":[46],"biomolecules":[48],"DelPhi,":[49],"which":[50],"widely":[52],"used":[53],"computational":[56],"biology":[57],"community.":[58],"algorithm":[60],"has":[61],"been":[62],"implemented":[63],"CUDA":[65],"tested":[67],"over":[68],"few":[70],"representative":[71],"cases":[72],"biological":[74],"interest.":[75],"Details":[76],"performance":[81],"test":[82],"results":[83],"are":[84],"illustrated.":[85],"speedup":[87],"~10":[89],"times":[90],"achieved":[92],"cases.":[99],"AVAILABILITY":[100],"AND":[101],"IMPLEMENTATION:":[102],"module":[104],"open-source":[106],"available":[108],"at":[109],"http://www.electrostaticszone.eu/index.php/downloads.":[110]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":3}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
