{"id":"https://openalex.org/W2944930475","doi":"https://doi.org/10.1093/nar/gkz378","title":"Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport","display_name":"Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport","publication_year":2019,"publication_date":"2019-05-06","ids":{"openalex":"https://openalex.org/W2944930475","doi":"https://doi.org/10.1093/nar/gkz378","mag":"2944930475","pmid":"https://pubmed.ncbi.nlm.nih.gov/31114897"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkz378","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz378","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W414/28880050/gkz378.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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/47/W1/W414/28880050/gkz378.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083252823","display_name":"Jan \u0160toura\u010d","orcid":"https://orcid.org/0000-0003-3139-3700"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210102302","display_name":"University Hospital Brno","ror":"https://ror.org/00qq1fp34","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210102302"]},{"id":"https://openalex.org/I4210136987","display_name":"St. Anne's University Hospital Brno","ror":"https://ror.org/049bjee35","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210136987"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Jan Stourac","raw_affiliation_strings":["International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic","Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic","institution_ids":["https://openalex.org/I4210102302","https://openalex.org/I4210136987"]},{"raw_affiliation_string":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021514188","display_name":"Ond\u0159ej V\u00e1vra","orcid":"https://orcid.org/0000-0003-1396-2543"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210102302","display_name":"University Hospital Brno","ror":"https://ror.org/00qq1fp34","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210102302"]},{"id":"https://openalex.org/I4210136987","display_name":"St. Anne's University Hospital Brno","ror":"https://ror.org/049bjee35","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210136987"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Ondrej Vavra","raw_affiliation_strings":["International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic","Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic","institution_ids":["https://openalex.org/I4210102302","https://openalex.org/I4210136987"]},{"raw_affiliation_string":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110558104","display_name":"Piia Kokkonen","orcid":null},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Piia Kokkonen","raw_affiliation_strings":["Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089216324","display_name":"Ji\u0159\u00ed Filipovi\u010d","orcid":"https://orcid.org/0000-0002-5703-9673"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210155092","display_name":"Czech Academy of Sciences, Institute of Computer Science","ror":"https://ror.org/0496n6574","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210155092"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Jiri Filipovic","raw_affiliation_strings":["Institute of Computer Science, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261","https://openalex.org/I4210155092"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010014308","display_name":"Gaspar Pinto","orcid":"https://orcid.org/0000-0002-8917-1169"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210102302","display_name":"University Hospital Brno","ror":"https://ror.org/00qq1fp34","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210102302"]},{"id":"https://openalex.org/I4210136987","display_name":"St. Anne's University Hospital Brno","ror":"https://ror.org/049bjee35","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210136987"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Gaspar Pinto","raw_affiliation_strings":["International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic","Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic","institution_ids":["https://openalex.org/I4210102302","https://openalex.org/I4210136987"]},{"raw_affiliation_string":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000513864","display_name":"Jan Brezovsk\u00fd","orcid":"https://orcid.org/0000-0001-9677-5078"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Jan Brezovsky","raw_affiliation_strings":["Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040585952","display_name":"Ji\u0159\u0131\u0301 Damborsk\u00fd","orcid":"https://orcid.org/0000-0002-7848-8216"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210102302","display_name":"University Hospital Brno","ror":"https://ror.org/00qq1fp34","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210102302"]},{"id":"https://openalex.org/I4210136987","display_name":"St. Anne's University Hospital Brno","ror":"https://ror.org/049bjee35","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210136987"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Jiri Damborsky","raw_affiliation_strings":["International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic","Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic","institution_ids":["https://openalex.org/I4210102302","https://openalex.org/I4210136987"]},{"raw_affiliation_string":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003693498","display_name":"David Bedn\u00e1\u0159","orcid":"https://orcid.org/0000-0002-6803-0340"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210102302","display_name":"University Hospital Brno","ror":"https://ror.org/00qq1fp34","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210102302"]},{"id":"https://openalex.org/I4210136987","display_name":"St. Anne's University Hospital Brno","ror":"https://ror.org/049bjee35","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210136987"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"David Bednar","raw_affiliation_strings":["International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic","Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"],"affiliations":[{"raw_affiliation_string":"International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic","institution_ids":["https://openalex.org/I4210102302","https://openalex.org/I4210136987"]},{"raw_affiliation_string":"Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5003693498"],"corresponding_institution_ids":["https://openalex.org/I21449261","https://openalex.org/I4210102302","https://openalex.org/I4210136987"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":7.9871,"has_fulltext":false,"cited_by_count":273,"citation_normalized_percentile":{"value":0.98304691,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"47","issue":"W1","first_page":"W414","last_page":"W422"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9979000091552734,"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":0.9979000091552734,"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/T13127","display_name":"Biotin and Related Studies","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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":0.9916999936103821,"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/graphical-user-interface","display_name":"Graphical user interface","score":0.802241325378418},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.712328314781189},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.6879001259803772},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6856561899185181},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.559754490852356},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.5261703729629517},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49785947799682617},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4291536808013916},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4210440218448639},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.3753964900970459},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3484123647212982},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2813875079154968},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.10423129796981812},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.0976330041885376}],"concepts":[{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.802241325378418},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.712328314781189},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.6879001259803772},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6856561899185181},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.559754490852356},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.5261703729629517},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49785947799682617},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4291536808013916},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4210440218448639},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.3753964900970459},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3484123647212982},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2813875079154968},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.10423129796981812},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0976330041885376},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"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}],"mesh":[{"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002352","descriptor_name":"Carrier Proteins","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":"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","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":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","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":"D020836","descriptor_name":"Protein Structure, Quaternary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020836","descriptor_name":"Protein Structure, Quaternary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020836","descriptor_name":"Protein Structure, Quaternary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkz378","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz378","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W414/28880050/gkz378.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:31114897","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31114897","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:europepmc.org:5577262","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6602463","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:is.muni.cz:1544938","is_oa":true,"landing_page_url":"https://is.muni.cz/publication/1544938","pdf_url":null,"source":{"id":"https://openalex.org/S4306400102","display_name":"Ve\u0159ejn\u00e9 slu\u017eby Informa\u010dn\u00edho syst\u00e9mu (Masarykiana Brunensis Universitas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"Nucleic acids research","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkz378","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz378","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W414/28880050/gkz378.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1169160269","display_name":null,"funder_award_id":"814418","funder_id":"https://openalex.org/F4320320306","funder_display_name":"European GNSS Agency"},{"id":"https://openalex.org/G3833704382","display_name":null,"funder_award_id":"720776","funder_id":"https://openalex.org/F4320320306","funder_display_name":"European GNSS Agency"}],"funders":[{"id":"https://openalex.org/F4320320306","display_name":"European GNSS Agency","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2944930475.pdf","grobid_xml":"https://content.openalex.org/works/W2944930475.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1570089161","https://openalex.org/W1757990252","https://openalex.org/W1966506605","https://openalex.org/W1966702876","https://openalex.org/W1987619816","https://openalex.org/W1988122552","https://openalex.org/W1993495903","https://openalex.org/W1999019158","https://openalex.org/W2001636605","https://openalex.org/W2011544982","https://openalex.org/W2011703027","https://openalex.org/W2019498797","https://openalex.org/W2030623529","https://openalex.org/W2038530231","https://openalex.org/W2047378557","https://openalex.org/W2051757997","https://openalex.org/W2057593004","https://openalex.org/W2067963143","https://openalex.org/W2104333254","https://openalex.org/W2105668062","https://openalex.org/W2110116688","https://openalex.org/W2112375320","https://openalex.org/W2115332677","https://openalex.org/W2119317961","https://openalex.org/W2120869341","https://openalex.org/W2122797035","https://openalex.org/W2126162505","https://openalex.org/W2134967712","https://openalex.org/W2137825366","https://openalex.org/W2140387095","https://openalex.org/W2144742694","https://openalex.org/W2154139219","https://openalex.org/W2161104561","https://openalex.org/W2164088236","https://openalex.org/W2169242540","https://openalex.org/W2169678694","https://openalex.org/W2171681733","https://openalex.org/W2277828430","https://openalex.org/W2317766861","https://openalex.org/W2331758362","https://openalex.org/W2521101013","https://openalex.org/W2549932119","https://openalex.org/W2561607416","https://openalex.org/W2765284721","https://openalex.org/W2789293857","https://openalex.org/W2801697388","https://openalex.org/W2802723872","https://openalex.org/W2804603144","https://openalex.org/W2805728727","https://openalex.org/W2835938797","https://openalex.org/W2889696754","https://openalex.org/W2898210859","https://openalex.org/W2902820054","https://openalex.org/W2910107890","https://openalex.org/W4233120011","https://openalex.org/W4234914623"],"related_works":["https://openalex.org/W2022968056","https://openalex.org/W3180179400","https://openalex.org/W2118366689","https://openalex.org/W1649706580","https://openalex.org/W2477652530","https://openalex.org/W2116888309","https://openalex.org/W2039055059","https://openalex.org/W3195608031","https://openalex.org/W2381088774","https://openalex.org/W2281900275"],"abstract_inverted_index":{"Caver":[0,25,55],"Web":[1,26],"1.0":[2,59],"is":[3,27,44,69,132,140,166],"a":[4,37,77,81,85,106,160],"web":[5],"server":[6,43,165],"for":[7,80,89,122,143,159],"comprehensive":[8,151],"analysis":[9],"of":[10,17,48,63,87],"protein":[11,78],"tunnels":[12],"and":[13,15,57,84,120,128,139,150],"channels,":[14],"study":[16,62],"the":[18,28,34,49,61,64,72,90,98,103,156],"ligands'":[19,123],"transport":[20,23,91],"through":[21],"these":[22],"pathways.":[24],"first":[29],"interactive":[30],"tool":[31,54,131,157],"allowing":[32],"both":[33],"analyses":[35],"within":[36],"single":[38],"graphical":[39,152],"user":[40,153],"interface.":[41],"The":[42,67,93,113,130,164],"built":[45],"on":[46],"top":[47],"abundantly":[50],"used":[51],"tunnel":[52,82],"detection":[53],"3.02":[56],"CaverDock":[58],"enabling":[60],"ligand":[65],"transport.":[66],"program":[68],"easy-to-use":[70],"as":[71],"only":[73],"required":[74],"inputs":[75],"are":[76],"structure":[79],"identification":[83],"list":[86],"ligands":[88],"analysis.":[92],"automated":[94],"guidance":[95],"procedures":[96],"assist":[97],"users":[99],"to":[100,108],"set":[101],"up":[102],"calculation":[104],"in":[105],"way":[107],"obtain":[109],"biologically":[110],"relevant":[111],"results.":[112],"identified":[114],"tunnels,":[115],"their":[116],"properties,":[117],"energy":[118],"profiles":[119],"trajectories":[121],"passages":[124],"can":[125],"be":[126],"calculated":[127],"visualized.":[129],"very":[133],"fast":[134],"(2-20":[135],"min":[136],"per":[137],"job)":[138],"applicable":[141],"even":[142],"virtual":[144],"screening":[145],"purposes.":[146],"Its":[147],"simple":[148],"setup":[149],"interface":[154],"make":[155],"accessible":[158],"broad":[161],"scientific":[162],"community.":[163],"freely":[167],"available":[168],"at":[169],"https://loschmidt.chemi.muni.cz/caverweb.":[170]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":58},{"year":2024,"cited_by_count":60},{"year":2023,"cited_by_count":54},{"year":2022,"cited_by_count":30},{"year":2021,"cited_by_count":34},{"year":2020,"cited_by_count":23},{"year":2019,"cited_by_count":6}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}