{"id":"https://openalex.org/W4411783921","doi":"https://doi.org/10.1021/acs.jcim.5c00821","title":"NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual","display_name":"NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual","publication_year":2025,"publication_date":"2025-06-30","ids":{"openalex":"https://openalex.org/W4411783921","doi":"https://doi.org/10.1021/acs.jcim.5c00821","pmid":"https://pubmed.ncbi.nlm.nih.gov/40586546"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00821","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00821","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.5c00821","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036716314","display_name":"Carlo Abate","orcid":"https://orcid.org/0000-0001-7024-3540"},"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"]},{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Carlo Abate","raw_affiliation_strings":["Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy","Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, via Belmeloro 6, 40126 Bologna, Italy"],"raw_orcid":"https://orcid.org/0000-0001-7024-3540","affiliations":[{"raw_affiliation_string":"Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, via Belmeloro 6, 40126 Bologna, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081015740","display_name":"Eleonora Serra","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"]},{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Eleonora Serra","raw_affiliation_strings":["Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy","Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, via Belmeloro 6, 40126 Bologna, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, via Belmeloro 6, 40126 Bologna, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","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":false,"raw_author_name":"Walter Rocchia","raw_affiliation_strings":["Concept Lab, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy"],"raw_orcid":"https://orcid.org/0000-0003-2480-7151","affiliations":[{"raw_affiliation_string":"Concept Lab, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy","institution_ids":["https://openalex.org/I30771326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021953983","display_name":"Andrea Cavalli","orcid":"https://orcid.org/0000-0002-6370-1176"},"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"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH","IT"],"is_corresponding":false,"raw_author_name":"Andrea Cavalli","raw_affiliation_strings":["Centre Europ\u00e9en de Calcul Atomique et Mol\u00e9culaire (CECAM)","Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy","Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne"],"raw_orcid":"https://orcid.org/0000-0002-6370-1176","affiliations":[{"raw_affiliation_string":"Centre Europ\u00e9en de Calcul Atomique et Mol\u00e9culaire (CECAM)","institution_ids":[]},{"raw_affiliation_string":"Computational & Chemical Biology, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"last","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":true,"raw_author_name":"Sergio Decherchi","raw_affiliation_strings":["Data Science and Computation Facility, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy"],"raw_orcid":"https://orcid.org/0000-0001-8371-2270","affiliations":[{"raw_affiliation_string":"Data Science and Computation Facility, Fondazione Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy","institution_ids":["https://openalex.org/I30771326"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5004937122","https://openalex.org/A5036716314"],"corresponding_institution_ids":["https://openalex.org/I30771326","https://openalex.org/I9360294"],"apc_list":null,"apc_paid":null,"fwci":4.7034,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.94593242,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"65","issue":"14","first_page":"7341","last_page":"7346"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12327","display_name":"Various Chemistry Research Topics","score":0.9872000217437744,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12327","display_name":"Various Chemistry Research Topics","score":0.9872000217437744,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9854000210762024,"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/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9226999878883362,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/surface","display_name":"Surface (topology)","score":0.5010178089141846},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.3854476511478424},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3652733564376831},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3510259985923767},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.2910233736038208},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09933874011039734}],"concepts":[{"id":"https://openalex.org/C2776799497","wikidata":"https://www.wikidata.org/wiki/Q484298","display_name":"Surface (topology)","level":2,"score":0.5010178089141846},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.3854476511478424},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3652733564376831},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3510259985923767},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2910233736038208},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09933874011039734},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","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}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.5c00821","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00821","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40586546","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40586546","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12308785","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12308785","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.5c00821","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00821","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W2022597857","https://openalex.org/W2030753552","https://openalex.org/W2059217294","https://openalex.org/W2095822427","https://openalex.org/W2123681603","https://openalex.org/W2140047797","https://openalex.org/W2271736303","https://openalex.org/W3083185352","https://openalex.org/W3090513030","https://openalex.org/W3099179819","https://openalex.org/W3140562424","https://openalex.org/W3213042299","https://openalex.org/W4285819878","https://openalex.org/W4378072282"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"Analyzing":[0],"molecular":[1,153],"surfaces":[2],"to":[3],"predict":[4],"functional":[5],"sites":[6,27],"and":[7,20,38,47,57,119,132,160],"identify":[8],"protein":[9,45],"cavities":[10],"for":[11,107,134,140,163],"small":[12],"molecule":[13],"binding":[14],"is":[15,176],"essential":[16],"in":[17,43],"structural":[18],"biology":[19],"drug":[21,49,170],"discovery,":[22],"particularly":[23],"when":[24],"targeting":[25],"allosteric":[26],"or":[28],"designing":[29],"PROTACs.":[30],"Moreover,":[31],"measuring":[32],"properties":[33],"like":[34],"volume,":[35],"surface":[36,56,118],"area,":[37],"pockets'":[39],"chemical":[40],"descriptors":[41],"helps":[42],"understanding":[44],"function":[46],"improving":[48],"development.":[50],"Over":[51],"the":[52,79,97,105,169],"past":[53],"decades,":[54],"numerous":[55],"pocket-detection":[58,120],"tools":[59,65],"have":[60],"been":[61],"developed.":[62],"While":[63],"these":[64],"provide":[66],"valuable":[67],"insights,":[68],"they":[69],"often":[70],"require":[71],"extensive":[72],"postprocessing":[73],"of":[74,100,168],"text":[75,109],"output":[76],"files,":[77],"making":[78],"analysis":[80],"workflow":[81],"cumbersome.":[82],"To":[83],"address":[84],"this":[85,155],"limitation,":[86],"we":[87],"introduce":[88],"NanoShaperWeb,":[89],"a":[90,126],"web":[91],"server":[92],"that":[93],"not":[94],"only":[95],"provides":[96],"computational":[98],"capabilities":[99],"NanoShaper":[101],"but":[102],"also":[103,138],"eliminates":[104],"need":[106],"manual":[108],"file":[110],"processing":[111],"through":[112],"an":[113,158],"intuitive":[114],"web-based":[115],"interface.":[116],"Molecular":[117],"computations":[121],"are":[122],"performed":[123],"remotely":[124],"via":[125],"queue,":[127],"with":[128,182],"results":[129],"visualized":[130],"interactively":[131],"available":[133],"download.":[135],"The":[136,173],"application":[137],"delivers":[139],"each":[141],"pocket":[142,149],"DrugPred":[143],"descriptors,":[144],"enabling":[145],"deeper":[146],"insights":[147],"into":[148],"features.":[150],"By":[151],"streamlining":[152],"analysis,":[154],"tool":[156,175],"offers":[157],"efficient":[159],"accessible":[161,178],"platform":[162],"researchers,":[164],"supporting":[165],"key":[166],"stages":[167],"design":[171],"pipeline.":[172],"NanoShaperWeb":[174],"freely":[177],"online":[179],"at":[180],"https://nanoshaperweb.iit.it/":[181],"no":[183],"required":[184],"registration.":[185]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
