{"id":"https://openalex.org/W2888970688","doi":"https://doi.org/10.1093/bioinformatics/bty761","title":"NanoShaper\u2013VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems","display_name":"NanoShaper\u2013VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems","publication_year":2018,"publication_date":"2018-08-30","ids":{"openalex":"https://openalex.org/W2888970688","doi":"https://doi.org/10.1093/bioinformatics/bty761","mag":"2888970688","pmid":"https://pubmed.ncbi.nlm.nih.gov/30169777"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty761","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty761","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/7/1241/48968449/bioinformatics_35_7_1241.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/35/7/1241/48968449/bioinformatics_35_7_1241.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004937122","display_name":"Sergio Decherchi","orcid":"https://orcid.org/0000-0001-8371-2270"},"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":"Sergio Decherchi","raw_affiliation_strings":["BiKi Technologies s.r.l., Genova, Italy","CONCEPT Lab, Istituto Italiano di Tecnologia, Genoa, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BiKi Technologies s.r.l., Genova, Italy","institution_ids":[]},{"raw_affiliation_string":"CONCEPT Lab, Istituto Italiano di Tecnologia, Genoa, Italy","institution_ids":["https://openalex.org/I30771326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049162857","display_name":"Andrea Spitaleri","orcid":"https://orcid.org/0000-0003-3012-3557"},"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":"Andrea Spitaleri","raw_affiliation_strings":["CONCEPT Lab, Istituto Italiano di Tecnologia, Genoa, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CONCEPT Lab, Istituto Italiano di Tecnologia, Genoa, Italy","institution_ids":["https://openalex.org/I30771326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048680880","display_name":"John E. Stone","orcid":"https://orcid.org/0000-0001-7215-762X"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Stone","raw_affiliation_strings":["Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"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":["CONCEPT Lab, Istituto Italiano di Tecnologia, Genoa, Italy"],"raw_orcid":"https://orcid.org/0000-0003-2480-7151","affiliations":[{"raw_affiliation_string":"CONCEPT Lab, Istituto Italiano di Tecnologia, Genoa, Italy","institution_ids":["https://openalex.org/I30771326"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"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":1.0257,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.73457607,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"35","issue":"7","first_page":"1241","last_page":"1243"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12285","display_name":"Surface Chemistry and Catalysis","score":0.8766000270843506,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12285","display_name":"Surface Chemistry and Catalysis","score":0.8766000270843506,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"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/T10913","display_name":"Molecular Junctions and Nanostructures","score":0.015300000086426735,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"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/T10578","display_name":"Supramolecular Chemistry and Complexes","score":0.01209999993443489,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7869946956634521},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7351151704788208},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6108584403991699},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5836854577064514},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5673243403434753},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5377154350280762},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5110541582107544},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4924863278865814},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.4584481418132782},{"id":"https://openalex.org/keywords/surface","display_name":"Surface (topology)","score":0.4360007345676422},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3529319167137146},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3325446844100952},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.30540311336517334},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2405666708946228},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1260419487953186},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.12544378638267517}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7869946956634521},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7351151704788208},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6108584403991699},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5836854577064514},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5673243403434753},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5377154350280762},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5110541582107544},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4924863278865814},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.4584481418132782},{"id":"https://openalex.org/C2776799497","wikidata":"https://www.wikidata.org/wiki/Q484298","display_name":"Surface (topology)","level":2,"score":0.4360007345676422},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3529319167137146},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3325446844100952},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30540311336517334},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2405666708946228},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1260419487953186},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.12544378638267517},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D036103","descriptor_name":"Nanotechnology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D036103","descriptor_name":"Nanotechnology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D036103","descriptor_name":"Nanotechnology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bty761","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty761","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/7/1241/48968449/bioinformatics_35_7_1241.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":"pmid:30169777","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30169777","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:europepmc.org:6057927","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6449750","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,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:air.unimi.it:2434/1041656","is_oa":true,"landing_page_url":"https://hdl.handle.net/2434/1041656","pdf_url":null,"source":{"id":"https://openalex.org/S4306400516","display_name":"Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189158943","host_organization_name":"University of Milan","host_organization_lineage":["https://openalex.org/I189158943"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty761","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty761","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/7/1241/48968449/bioinformatics_35_7_1241.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/G1104241873","display_name":null,"funder_award_id":"P41 GM104601","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"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/G3644531907","display_name":"Center for Macromolecular Modeling and Bioinformatics","funder_award_id":"5p41gm104601-32","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5328185380","display_name":null,"funder_award_id":"GM104601","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5426103414","display_name":null,"funder_award_id":"1R01GM093937","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5907587529","display_name":null,"funder_award_id":"1R01GM093937-01","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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2888970688.pdf","grobid_xml":"https://content.openalex.org/works/W2888970688.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W98257838","https://openalex.org/W1991074394","https://openalex.org/W2022597857","https://openalex.org/W2029667189","https://openalex.org/W2031305384","https://openalex.org/W2036381880","https://openalex.org/W2043901383","https://openalex.org/W2103092699","https://openalex.org/W2112794559","https://openalex.org/W2131080603","https://openalex.org/W2516083692","https://openalex.org/W2744078451"],"related_works":["https://openalex.org/W2618286804","https://openalex.org/W2329643025","https://openalex.org/W3131163342","https://openalex.org/W2166271660","https://openalex.org/W2092256833","https://openalex.org/W2142369114","https://openalex.org/W2002770077","https://openalex.org/W2361728394","https://openalex.org/W2352631095","https://openalex.org/W2408577762"],"abstract_inverted_index":{"SUMMARY:":[0],"NanoShaper":[1,42,103],"is":[2,127],"a":[3,61,86],"program":[4],"specifically":[5],"aiming":[6],"the":[7,12,36,39,67,74,77,90,92,98,109],"construction":[8],"and":[9,23,33,135],"analysis":[10],"of":[11,15,35,49,69,76,89,100],"molecular":[13,55,101,112],"surface":[14,45],"nanoscopic":[16],"systems.":[17],"It":[18,57],"uses":[19],"ray-casting":[20],"for":[21,52],"parallelism":[22],"it":[24],"performs":[25],"analytical":[26],"computations":[27],"whenever":[28],"possible":[29],"to":[30,73],"maximize":[31],"robustness":[32],"accuracy":[34],"approach.":[37],"Among":[38],"other":[40],"features,":[41],"provides":[43],"volume,":[44],"area,":[46],"including":[47],"that":[48],"internal":[50],"cavities,":[51],"any":[53],"considered":[54],"system.":[56],"identifies":[58],"pockets":[59],"via":[60],"very":[62],"intuitive":[63],"definition":[64,75],"based":[65],"on":[66],"concept":[68],"probe":[70],"radius,":[71],"intrinsic":[72],"solvent":[78],"excluded":[79],"surface.":[80],"We":[81],"show":[82],"here":[83],"that,":[84],"with":[85,108],"suitable":[87],"choice":[88],"parameters,":[91],"same":[93],"approach":[94],"can":[95],"also":[96],"permit":[97],"visualisation":[99],"channels.":[102],"has":[104],"now":[105],"been":[106],"interfaced":[107],"widely":[110],"used":[111],"visualization":[113],"software":[114],"VMD,":[115],"further":[116],"enriching":[117],"its":[118,132],"already":[119],"well":[120],"furnished":[121],"toolset.":[122],"AVAILABILITY":[123],"AND":[124],"IMPLEMENTATION:":[125],"VMD":[126],"available":[128,139,147],"at":[129,140,148],"http://www.ks.uiuc.edu/Research/vmd/.":[130],"NanoShaper,":[131],"documentation,":[133],"tutorials":[134],"supporting":[136],"programs":[137],"are":[138,146],"http://concept.iit.it/downloads.":[141],"SUPPLEMENTARY":[142],"INFORMATION:":[143],"Supplementary":[144],"data":[145],"Bioinformatics":[149],"online.":[150]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
