{"id":"https://openalex.org/W2996648992","doi":"https://doi.org/10.1093/bioinformatics/btz946","title":"AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective","display_name":"AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective","publication_year":2019,"publication_date":"2019-12-17","ids":{"openalex":"https://openalex.org/W2996648992","doi":"https://doi.org/10.1093/bioinformatics/btz946","mag":"2996648992","pmid":"https://pubmed.ncbi.nlm.nih.gov/31860077","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/7178393"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz946","doi":"https://doi.org/10.1093/bioinformatics/btz946","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz946","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2599/33116512/btz946.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2599/33116512/btz946.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082184781","display_name":"Tomasz Magdziarz","orcid":"https://orcid.org/0000-0002-2904-6788","observed_orcids":["https://orcid.org/0000-0002-2904-6788"]},"institutions":[{"id":"https://openalex.org/I119004910","display_name":"Silesian University of Technology","ror":"https://ror.org/02dyjk442","country_code":"PL","type":"education","lineage":["https://openalex.org/I119004910"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Tomasz Magdziarz","raw_affiliation_strings":["Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland","institution_ids":["https://openalex.org/I119004910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017399776","display_name":"Karolina Mitusi\u0144ska","orcid":"https://orcid.org/0000-0002-0183-0845","observed_orcids":["https://orcid.org/0000-0002-0183-0845"]},"institutions":[{"id":"https://openalex.org/I119004910","display_name":"Silesian University of Technology","ror":"https://ror.org/02dyjk442","country_code":"PL","type":"education","lineage":["https://openalex.org/I119004910"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Karolina Mitusi\u0144ska","raw_affiliation_strings":["Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland","institution_ids":["https://openalex.org/I119004910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034635429","display_name":"Maria Bz\u00f3wka","orcid":"https://orcid.org/0000-0001-6802-8753","observed_orcids":["https://orcid.org/0000-0001-6802-8753"]},"institutions":[{"id":"https://openalex.org/I119004910","display_name":"Silesian University of Technology","ror":"https://ror.org/02dyjk442","country_code":"PL","type":"education","lineage":["https://openalex.org/I119004910"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Maria Bz\u00f3wka","raw_affiliation_strings":["Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland","institution_ids":["https://openalex.org/I119004910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021846019","display_name":"Agata Raczy\u0144ska","orcid":"https://orcid.org/0000-0002-1884-3669","observed_orcids":["https://orcid.org/0000-0002-1884-3669"]},"institutions":[{"id":"https://openalex.org/I119004910","display_name":"Silesian University of Technology","ror":"https://ror.org/02dyjk442","country_code":"PL","type":"education","lineage":["https://openalex.org/I119004910"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Agata Raczy\u0144ska","raw_affiliation_strings":["Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland","institution_ids":["https://openalex.org/I119004910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021835274","display_name":"Agnieszka Sta\u0144czak","orcid":"https://orcid.org/0000-0002-5335-1387","observed_orcids":["https://orcid.org/0000-0002-5335-1387"]},"institutions":[{"id":"https://openalex.org/I119004910","display_name":"Silesian University of Technology","ror":"https://ror.org/02dyjk442","country_code":"PL","type":"education","lineage":["https://openalex.org/I119004910"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Agnieszka Sta\u0144czak","raw_affiliation_strings":["Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland","institution_ids":["https://openalex.org/I119004910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007091311","display_name":"Micha\u0142 Bana\u015b","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I119004910","display_name":"Silesian University of Technology","ror":"https://ror.org/02dyjk442","country_code":"PL","type":"education","lineage":["https://openalex.org/I119004910"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Micha\u0142 Banas","raw_affiliation_strings":["Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland","institution_ids":["https://openalex.org/I119004910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080613493","display_name":"Weronika Bagrowska","orcid":"https://orcid.org/0000-0003-1749-8514","observed_orcids":["https://orcid.org/0000-0003-1749-8514"]},"institutions":[{"id":"https://openalex.org/I119004910","display_name":"Silesian University of Technology","ror":"https://ror.org/02dyjk442","country_code":"PL","type":"education","lineage":["https://openalex.org/I119004910"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Weronika Bagrowska","raw_affiliation_strings":["Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland","institution_ids":["https://openalex.org/I119004910"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059334774","display_name":"Artur G\u00f3ra","orcid":"https://orcid.org/0000-0003-2530-6957","observed_orcids":["https://orcid.org/0000-0003-2530-6957"]},"institutions":[{"id":"https://openalex.org/I119004910","display_name":"Silesian University of Technology","ror":"https://ror.org/02dyjk442","country_code":"PL","type":"education","lineage":["https://openalex.org/I119004910"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Artur G\u00f3ra","raw_affiliation_strings":["Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tunneling Group, Biotechnology Centre, Silesian University of Technology , 44-100 Gliwice, Poland","institution_ids":["https://openalex.org/I119004910"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5059334774"],"corresponding_institution_ids":["https://openalex.org/I119004910"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":1.4884,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.82363361,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"8","first_page":"2599","last_page":"2601"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9038000106811523,"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":0.9038000106811523,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.06759999692440033,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.02199999988079071,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-tunnels","display_name":"protein tunnels","score":0.5490000247955322},{"id":"https://openalex.org/keywords/protein-pores","display_name":"protein pores","score":0.6610000133514404},{"id":"https://openalex.org/keywords/channel-proteins","display_name":"protein channels","score":0.7599999904632568},{"id":"https://openalex.org/keywords/binding-pocket","display_name":"binding pocket","score":0.7799999713897705},{"id":"https://openalex.org/keywords/ligand-transport","display_name":"ligand transport","score":0.734000027179718},{"id":"https://openalex.org/keywords/protein-engineering","display_name":"protein engineering","score":0.8690000176429749},{"id":"https://openalex.org/keywords/drug-design","display_name":"drug design","score":0.9980000257492065}],"concepts":[{"id":"https://openalex.org/C204389451","wikidata":"https://www.wikidata.org/wiki/Q178593","display_name":"Macromolecule","level":2,"score":0.8495092988014221},{"id":"https://openalex.org/C75079739","wikidata":"https://www.wikidata.org/wiki/Q1571801","display_name":"Intramolecular force","level":2,"score":0.796867311000824},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.5506576299667358},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5376812815666199},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3843352198600769},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.3733879625797272},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3378313481807709},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3086808919906616},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17605775594711304},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16600993275642395},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13317987322807312},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.1294095814228058}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz946","doi":"https://doi.org/10.1093/bioinformatics/btz946","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz946","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2599/33116512/btz946.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7178393","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7178393","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmid:31860077","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31860077","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,"listed_in":[],"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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz946","doi":"https://doi.org/10.1093/bioinformatics/btz946","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz946","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2599/33116512/btz946.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2181572660","display_name":null,"funder_award_id":"DEC-2015/18/M/NZ1/00427","funder_id":"https://openalex.org/F4320322650","funder_display_name":"Narodowym Centrum Nauki"},{"id":"https://openalex.org/G3375065197","display_name":null,"funder_award_id":"2013/10/E/NZ1/00649","funder_id":"https://openalex.org/F4320322650","funder_display_name":"Narodowym Centrum Nauki"},{"id":"https://openalex.org/G5085543109","display_name":null,"funder_award_id":"DEC-2013/10/E/NZ1/00649","funder_id":"https://openalex.org/F4320322650","funder_display_name":"Narodowym Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320322650","display_name":"Narodowym Centrum Nauki","ror":"https://ror.org/03ha2q922"},{"id":"https://openalex.org/F4320326815","display_name":"Infrastruktura PL-Grid","ror":"https://ror.org/01m3qaz74"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2996648992.pdf","grobid_xml":"https://content.openalex.org/works/W2996648992.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2074512072","https://openalex.org/W2104333254","https://openalex.org/W2171075097","https://openalex.org/W2343614482","https://openalex.org/W2501046342","https://openalex.org/W2519539312","https://openalex.org/W2593483581","https://openalex.org/W2611419564","https://openalex.org/W2611735159","https://openalex.org/W2789293857","https://openalex.org/W2894715629","https://openalex.org/W2942491534","https://openalex.org/W3178334431"],"related_works":["https://openalex.org/W2593483581","https://openalex.org/W3178966173","https://openalex.org/W3134651789","https://openalex.org/W2801697388","https://openalex.org/W119714159","https://openalex.org/W2141891891","https://openalex.org/W2944202352","https://openalex.org/W2944930475","https://openalex.org/W4206907955","https://openalex.org/W3005725774"],"abstract_inverted_index":{"MOTIVATION:":[0],"Tunnels,":[1],"pores,":[2],"channels,":[3],"pockets":[4],"and":[5,11,15,20,49,83,87,96],"cavities":[6,23],"contribute":[7],"to":[8,29,41,100],"proteins":[9,36],"architecture":[10],"performance.":[12],"However,":[13],"analysis":[14,34,62],"characteristics":[16],"of":[17,35,81,93],"transportation":[18,47],"pathways":[19],"internal":[21],"binding":[22,50],"are":[24,111],"performed":[25],"separately.":[26],"We":[27],"aimed":[28],"provide":[30],"universal":[31],"tool":[32],"for":[33,60],"integral":[37],"interior":[38],"with":[39],"access":[40],"detailed":[42],"information":[43],"on":[44],"the":[45,64,91,94],"ligands":[46,70],"phenomena":[48],"preferences.":[51],"RESULTS:":[52],"AQUA-DUCT":[53],"version":[54,75],"1.0":[55],"is":[56],"a":[57],"comprehensive":[58],"method":[59],"macromolecules":[61,82],"from":[63],"intramolecular":[65],"voids":[66],"perspective":[67],"using":[68],"small":[69,101],"as":[71],"molecular":[72],"probes.":[73],"This":[74],"gives":[76],"insight":[77],"into":[78],"several":[79],"properties":[80],"facilitates":[84],"protein":[85],"engineering":[86],"drug":[88],"design":[89],"by":[90],"combination":[92],"tracking":[95],"local":[97],"mapping":[98],"approach":[99],"ligands.":[102],"AVAILABILITY":[103],"AND":[104],"IMPLEMENTATION:":[105],"http://www.aquaduct.pl.":[106],"SUPPLEMENTARY":[107],"INFORMATION:":[108],"Supplementary":[109],"data":[110],"available":[112],"at":[113],"Bioinformatics":[114],"online.":[115]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":8}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2019-12-26T00:00:00"}