{"id":"https://openalex.org/W2153255725","doi":"https://doi.org/10.1093/nar/gkl206","title":"GRAMM-X public web server for protein-protein docking","display_name":"GRAMM-X public web server for protein-protein docking","publication_year":2006,"publication_date":"2006-07-01","ids":{"openalex":"https://openalex.org/W2153255725","doi":"https://doi.org/10.1093/nar/gkl206","mag":"2153255725","pmid":"https://pubmed.ncbi.nlm.nih.gov/16845016"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkl206","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl206","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W310/7623130/gkl206.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W310/7623130/gkl206.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067042263","display_name":"Andrey Tovchigrechko","orcid":"https://orcid.org/0000-0002-0959-4429"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]},{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"A. Tovchigrechko","raw_affiliation_strings":["Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA. andrey@ku.edu","Center for Bioinformatics and and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA. andrey@ku.edu","institution_ids":["https://openalex.org/I146416000"]},{"raw_affiliation_string":"Center for Bioinformatics and and","institution_ids":["https://openalex.org/I4210148697"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013394507","display_name":"Ilya A. Vakser","orcid":"https://orcid.org/0000-0002-5743-2934"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]},{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"I. A. Vakser","raw_affiliation_strings":["Center for Bioinformatics and and","Department of Molecular Biosciences, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and and","institution_ids":["https://openalex.org/I4210148697"]},{"raw_affiliation_string":"Department of Molecular Biosciences, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA","institution_ids":["https://openalex.org/I146416000"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":7.9096,"has_fulltext":true,"cited_by_count":817,"citation_normalized_percentile":{"value":0.98272034,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"34","issue":"Web Server","first_page":"W310","last_page":"W314"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.986299991607666,"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":0.986299991607666,"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":0.9804999828338623,"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/T12827","display_name":"Biochemical and Molecular Research","score":0.967199981212616,"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/docking","display_name":"Docking (animal)","score":0.7604625225067139},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.7310448884963989},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6636089086532593},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5452313423156738},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5321435332298279},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5294620394706726},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.4966662526130676},{"id":"https://openalex.org/keywords/macromolecular-docking","display_name":"Macromolecular docking","score":0.4219288229942322},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.32110416889190674},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.2945006191730499},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.22726580500602722},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12015092372894287}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7604625225067139},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.7310448884963989},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6636089086532593},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5452313423156738},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5321435332298279},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5294620394706726},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.4966662526130676},{"id":"https://openalex.org/C116887118","wikidata":"https://www.wikidata.org/wiki/Q836685","display_name":"Macromolecular docking","level":3,"score":0.4219288229942322},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.32110416889190674},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.2945006191730499},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.22726580500602722},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12015092372894287},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkl206","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl206","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W310/7623130/gkl206.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16845016","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16845016","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.969.9187","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.969.9187","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://kuscholarworks.ku.edu/bitstream/handle/1808/17606/VakserI_NAR_34%282%29W310.pdf%3Bjsessionid%3D20BE0721D379786D88E50A3D3B2A09E5?sequence%3D1","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.980.849","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.980.849","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/34/suppl_2/W310.full.pdf","raw_type":"text"},{"id":"pmh:oai:kuscholarworks.ku.edu:1808/17606","is_oa":true,"landing_page_url":"http://hdl.handle.net/1808/17606","pdf_url":null,"source":{"id":"https://openalex.org/S4306400421","display_name":"KU ScholarWorks (The University of Kansas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I146416000","host_organization_name":"University of Kansas","host_organization_lineage":["https://openalex.org/I146416000"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1538913","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkl206","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkl206","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl206","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W310/7623130/gkl206.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.47999998927116394,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2153255725.pdf","grobid_xml":"https://content.openalex.org/works/W2153255725.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W587397701","https://openalex.org/W1483944095","https://openalex.org/W1997865081","https://openalex.org/W2000383223","https://openalex.org/W2000464453","https://openalex.org/W2016333765","https://openalex.org/W2092360980","https://openalex.org/W2093954175","https://openalex.org/W2095761477","https://openalex.org/W2105438341","https://openalex.org/W2112743424","https://openalex.org/W2114817191","https://openalex.org/W2118459915","https://openalex.org/W2123028643","https://openalex.org/W2131313124","https://openalex.org/W2132709044","https://openalex.org/W2151460035","https://openalex.org/W2160514392","https://openalex.org/W2163462520","https://openalex.org/W2174242780","https://openalex.org/W3000073799"],"related_works":["https://openalex.org/W2996908194","https://openalex.org/W2585040066","https://openalex.org/W2162380182","https://openalex.org/W3187431608","https://openalex.org/W3005126098","https://openalex.org/W2157273785","https://openalex.org/W2064383522","https://openalex.org/W2942988621","https://openalex.org/W2140522686","https://openalex.org/W3158075195"],"abstract_inverted_index":{"Protein":[0],"docking":[1,46],"software":[2,37],"GRAMM-X":[3,52],"and":[4,23,38,74],"its":[5],"web":[6,27],"interface":[7],"(http://vakser.bioinformatics.ku.edu/resources/gramm/grammx)":[8],"extend":[9],"the":[10,77],"original":[11],"GRAMM":[12],"Fast":[13],"Fourier":[14],"Transformation":[15],"methodology":[16],"by":[17,56,67],"employing":[18],"smoothed":[19],"potentials,":[20],"refinement":[21],"stage,":[22],"knowledge-based":[24],"scoring.":[25],"The":[26,62],"server":[28,53,63,79],"frees":[29],"users":[30],"from":[31],"complex":[32],"installation":[33],"of":[34,71],"database-dependent":[35],"parallel":[36],"maintaining":[39],"large":[40],"hardware":[41],"resources":[42],"needed":[43],"for":[44],"protein":[45],"simulations.":[47],"Docking":[48],"problems":[49],"submitted":[50],"to":[51],"are":[54],"processed":[55],"a":[57],"320":[58],"processor":[59],"Linux":[60],"cluster.":[61],"was":[64],"extensively":[65],"tested":[66],"benchmarking,":[68],"several":[69],"months":[70],"public":[72],"use,":[73],"participation":[75],"in":[76],"CAPRI":[78],"track.":[80]},"counts_by_year":[{"year":2026,"cited_by_count":20},{"year":2025,"cited_by_count":37},{"year":2024,"cited_by_count":61},{"year":2023,"cited_by_count":37},{"year":2022,"cited_by_count":64},{"year":2021,"cited_by_count":49},{"year":2020,"cited_by_count":60},{"year":2019,"cited_by_count":66},{"year":2018,"cited_by_count":40},{"year":2017,"cited_by_count":51},{"year":2016,"cited_by_count":50},{"year":2015,"cited_by_count":34},{"year":2014,"cited_by_count":46},{"year":2013,"cited_by_count":47},{"year":2012,"cited_by_count":37}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
