{"id":"https://openalex.org/W2157040708","doi":"https://doi.org/10.1186/1758-2946-5-36","title":"The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites","display_name":"The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites","publication_year":2013,"publication_date":"2013-07-29","ids":{"openalex":"https://openalex.org/W2157040708","doi":"https://doi.org/10.1186/1758-2946-5-36","mag":"2157040708","pmid":"https://pubmed.ncbi.nlm.nih.gov/23895374"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-5-36","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-36","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-36","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-36","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073519245","display_name":"Adri\u00e0 Cereto\u2010Massagu\u00e9","orcid":"https://orcid.org/0000-0002-9319-6377"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universidad Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Adri\u00e0 Cereto-Massagu\u00e9","raw_affiliation_strings":["Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia 43007, Spain. gerard.pujadas@urv.cat","Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia 43007, Spain. gerard.pujadas@urv.cat","institution_ids":[]},{"raw_affiliation_string":"Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain","institution_ids":["https://openalex.org/I55952717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024115537","display_name":"Mar\u00eda Jos\u00e9 Ojeda","orcid":"https://orcid.org/0000-0002-9290-1935"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universidad Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Mar\u00eda Jos\u00e9 Ojeda","raw_affiliation_strings":["Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain","institution_ids":["https://openalex.org/I55952717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040824480","display_name":"Robbie P. Joosten","orcid":"https://orcid.org/0000-0002-2323-2686"},"institutions":[{"id":"https://openalex.org/I2898336195","display_name":"The Netherlands Cancer Institute","ror":"https://ror.org/03xqtf034","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2898336195"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Robbie P Joosten","raw_affiliation_strings":["Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands","institution_ids":["https://openalex.org/I2898336195"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050713208","display_name":"Cristina Valls","orcid":"https://orcid.org/0000-0001-5583-5695"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universidad Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Cristina Valls","raw_affiliation_strings":["Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain","institution_ids":["https://openalex.org/I55952717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041082378","display_name":"Miquel Mulero","orcid":"https://orcid.org/0000-0003-2545-2065"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universidad Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Miquel Mulero","raw_affiliation_strings":["Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain","institution_ids":["https://openalex.org/I55952717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008403454","display_name":"M. Josepa Salvad\u00f3","orcid":"https://orcid.org/0000-0003-3883-3326"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universidad Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"M Josepa Salvado","raw_affiliation_strings":["Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain","institution_ids":["https://openalex.org/I55952717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001243528","display_name":"Anna Arola\u2010Arnal","orcid":"https://orcid.org/0000-0001-6529-1345"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universidad Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Anna Arola-Arnal","raw_affiliation_strings":["Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain","institution_ids":["https://openalex.org/I55952717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003416093","display_name":"Llu\u0131\u0301s Arola","orcid":"https://orcid.org/0000-0003-2767-1974"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universidad Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]},{"id":"https://openalex.org/I4210095834","display_name":"Technological Center of Nutrition and Health","ror":"https://ror.org/00mzj5z57","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210095834"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Llu\u00eds Arola","raw_affiliation_strings":["Centre Tecnol\u00f2gic de Nutrici\u00f3 i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat 1, Reus, Catalonia, 43204, Spain","Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre Tecnol\u00f2gic de Nutrici\u00f3 i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat 1, Reus, Catalonia, 43204, Spain","institution_ids":["https://openalex.org/I4210095834"]},{"raw_affiliation_string":"Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain","institution_ids":["https://openalex.org/I55952717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003374296","display_name":"Santiago Garc\u0131\u0301a-Vallv\u00e9","orcid":"https://orcid.org/0000-0002-0348-7497"},"institutions":[{"id":"https://openalex.org/I4210095834","display_name":"Technological Center of Nutrition and Health","ror":"https://ror.org/00mzj5z57","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210095834"]},{"id":"https://openalex.org/I55952717","display_name":"Universidad Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Santiago Garcia-Vallv\u00e9","raw_affiliation_strings":["Centre Tecnol\u00f2gic de Nutrici\u00f3 i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat 1, Reus, Catalonia, 43204, Spain","Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre Tecnol\u00f2gic de Nutrici\u00f3 i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat 1, Reus, Catalonia, 43204, Spain","institution_ids":["https://openalex.org/I4210095834"]},{"raw_affiliation_string":"Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain","institution_ids":["https://openalex.org/I55952717"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089370543","display_name":"Gerard Pujadas","orcid":"https://orcid.org/0000-0003-2598-8089"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universidad Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]},{"id":"https://openalex.org/I4210095834","display_name":"Technological Center of Nutrition and Health","ror":"https://ror.org/00mzj5z57","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210095834"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Gerard Pujadas","raw_affiliation_strings":["Centre Tecnol\u00f2gic de Nutrici\u00f3 i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat 1, Reus, Catalonia, 43204, Spain","Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre Tecnol\u00f2gic de Nutrici\u00f3 i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat 1, Reus, Catalonia, 43204, Spain","institution_ids":["https://openalex.org/I4210095834"]},{"raw_affiliation_string":"Grup de Recerca en Nutrigen\u00f2mica, Departament de Bioqu\u00edmica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marce\u0140l\u00ed Domingo s/n, Tarragona, Catalonia, 43007, Spain","institution_ids":["https://openalex.org/I55952717"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5073519245"],"corresponding_institution_ids":["https://openalex.org/I55952717"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":2.4552,"has_fulltext":true,"cited_by_count":48,"citation_normalized_percentile":{"value":0.89674177,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"5","issue":"1","first_page":"36","last_page":"36"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.8313999772071838,"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"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.8313999772071838,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.06440000236034393,"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":0.04749999940395355,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.8404167890548706},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.7732334136962891},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5913718342781067},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5575523972511292},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5016598701477051},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.4705736041069031},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4587670862674713},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3551028370857239},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3373585343360901},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.30962538719177246},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2638240158557892},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.14374953508377075},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10768041014671326}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.8404167890548706},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.7732334136962891},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5913718342781067},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5575523972511292},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5016598701477051},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.4705736041069031},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4587670862674713},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3551028370857239},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3373585343360901},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.30962538719177246},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2638240158557892},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.14374953508377075},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10768041014671326},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","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}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-5-36","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-36","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-36","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Cheminformatics","raw_type":"journal-article"},{"id":"pmid:23895374","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23895374","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 cheminformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2726876","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3733808","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"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-5-36","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-36","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-36","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"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 Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4099999964237213,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G8667726325","display_name":null,"funder_award_id":"722.011.011","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320314041","display_name":"St. Olaf College","ror":"https://ror.org/01q7w1f47"},{"id":"https://openalex.org/F4320321505","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2157040708.pdf","grobid_xml":"https://content.openalex.org/works/W2157040708.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1557986018","https://openalex.org/W1983194490","https://openalex.org/W1984002179","https://openalex.org/W1995808589","https://openalex.org/W1998000033","https://openalex.org/W2004461664","https://openalex.org/W2007697641","https://openalex.org/W2013083986","https://openalex.org/W2018127105","https://openalex.org/W2018661561","https://openalex.org/W2020300078","https://openalex.org/W2045777307","https://openalex.org/W2065929501","https://openalex.org/W2066620371","https://openalex.org/W2075393035","https://openalex.org/W2078217908","https://openalex.org/W2079847644","https://openalex.org/W2087278791","https://openalex.org/W2099099776","https://openalex.org/W2105174531","https://openalex.org/W2108627006","https://openalex.org/W2108921801","https://openalex.org/W2124464974","https://openalex.org/W2130253098","https://openalex.org/W2130479394","https://openalex.org/W2131639373","https://openalex.org/W2147085530","https://openalex.org/W2153376167","https://openalex.org/W2154994578","https://openalex.org/W2159707853","https://openalex.org/W2401430279","https://openalex.org/W2488230902","https://openalex.org/W2786774014","https://openalex.org/W4210309881"],"related_works":["https://openalex.org/W2020669016","https://openalex.org/W2088162897","https://openalex.org/W2090630809","https://openalex.org/W2106612397","https://openalex.org/W4387804157","https://openalex.org/W2518314460","https://openalex.org/W2589205199","https://openalex.org/W2119891507","https://openalex.org/W2089869950","https://openalex.org/W2047544230"],"abstract_inverted_index":{"BACKGROUND:":[0],"Many":[1],"Protein":[2],"Data":[3],"Bank":[4],"(PDB)":[5],"users":[6,101,231],"assume":[7],"that":[8,19,86],"the":[9,25,42,61,72,90,127,137,140,162,197,208,211,218,234,238,244],"deposited":[10],"structural":[11],"models":[12,21,39,70,134,254],"are":[13,22,179],"of":[14,27,32,63,92,143,158,164,210,213],"high":[15],"quality":[16,62,209],"but":[17],"forget":[18],"these":[20],"derived":[23],"from":[24,71,135],"interpretation":[26],"experimental":[28,245],"data.":[29,246],"The":[30,75,149,200],"accuracy":[31],"atom":[33],"coordinates":[34,97,124,165,240],"is":[35,84,202,248],"not":[36],"homogeneous":[37],"between":[38],"or":[40,104,139,193],"throughout":[41],"same":[43],"model.":[44],"To":[45],"avoid":[46],"basing":[47],"a":[48,52,57,109,156],"research":[49],"project":[50],"on":[51,196],"flawed":[53],"model,":[54],"we":[55],"present":[56],"tool":[58],"for":[59,78,98,155,255,258],"assessing":[60],"ligands":[64,189,216],"and":[65,80,95,121,145,176,188,215,222,237,267],"binding":[66,93,122,235],"sites":[67],"in":[68,241],"crystallographic":[69,147],"PDB.":[73],"RESULTS:":[74],"Validation":[76],"HElper":[77],"LIgands":[79],"Binding":[81],"Sites":[82],"(VHELIBS)":[83],"software":[85],"aims":[87],"to":[88,117,126,161,166,205,217,232,243,252],"ease":[89],"validation":[91],"site":[94,123,236],"ligand":[96,120,239],"non-crystallographers":[99],"(i.e.,":[100],"with":[102],"little":[103],"no":[105],"crystallography":[106],"knowledge).":[107],"Using":[108],"convenient":[110],"graphical":[111],"user":[112,150,201],"interface,":[113],"it":[114],"allows":[115,229],"one":[116],"check":[118,207],"how":[119],"fit":[125,163,212],"electron":[128,167,219],"density":[129,168,220],"map.":[130],"VHELIBS":[131,183,228],"can":[132,151],"use":[133],"either":[136],"PDB":[138],"PDB_REDO":[141],"databank":[142],"re-refined":[144],"re-built":[146],"models.":[148],"specify":[152],"threshold":[153],"values":[154],"series":[157],"properties":[159],"related":[160],"(Real":[169],"Space":[170,173],"R,":[171],"Real":[172],"Correlation":[174],"Coefficient":[175],"average":[177],"occupancy":[178],"used":[180],"by":[181],"default).":[182],"will":[184],"automatically":[185],"classify":[186],"residues":[187,214],"as":[190,263],"Good,":[191],"Dubious":[192],"Bad":[194],"based":[195],"specified":[198],"limits.":[199],"also":[203],"able":[204],"visually":[206],"map":[221],"reclassify":[223],"them":[224],"if":[225],"needed.":[226],"CONCLUSIONS:":[227],"inexperienced":[230],"examine":[233],"relation":[242],"This":[247],"an":[249],"important":[250],"step":[251],"evaluate":[253],"their":[256],"fitness":[257],"drug":[259],"discovery":[260],"purposes":[261],"such":[262],"structure-based":[264],"pharmacophore":[265],"development":[266],"protein-ligand":[268],"docking":[269],"experiments.":[270]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
