{"id":"https://openalex.org/W7119899366","doi":"https://doi.org/10.1186/s13321-026-01154-0","title":"Analysis of cyclohexane, cyclopentane, and benzene conformations in ligands for PDB X-ray structures using the Hill-Reilly approach","display_name":"Analysis of cyclohexane, cyclopentane, and benzene conformations in ligands for PDB X-ray structures using the Hill-Reilly approach","publication_year":2026,"publication_date":"2026-01-10","ids":{"openalex":"https://openalex.org/W7119899366","doi":"https://doi.org/10.1186/s13321-026-01154-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/41519762"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-026-01154-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01154-0","pdf_url":null,"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://doi.org/10.1186/s13321-026-01154-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5099430632","display_name":"Gabriela Bu\u010dekov\u00e1","orcid":"https://orcid.org/0009-0000-3623-718X"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"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":"Gabriela Bu\u010dekov\u00e1","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5099430633","display_name":"Viktoriia Doshchenko","orcid":null},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"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":"Viktoriia Doshchenko","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102997614","display_name":"Tom\u00e1\u0161 Svoboda","orcid":"https://orcid.org/0009-0006-3773-3082"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"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":"Tom\u00e1\u0161 Svoboda","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093952430","display_name":"Jana Porubsk\u00e1","orcid":"https://orcid.org/0009-0003-7074-4638"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"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":"Jana Porubsk\u00e1","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067978620","display_name":"Aliaksei Chareshneu","orcid":"https://orcid.org/0000-0002-4323-2130"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Aliaksei Chareshneu","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040326443","display_name":"Tom\u00e1\u0161 Ra\u010dek","orcid":"https://orcid.org/0000-0002-0296-2452"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"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":"Tom\u00e1\u0161 Ra\u010dek","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025266471","display_name":"Vladim\u00edr Horsk\u00fd","orcid":"https://orcid.org/0000-0002-9252-5386"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"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":"Vladim\u00edr Horsk\u00fd","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. vladimir.horsky@mail.muni.cz","National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. vladimir.horsky@mail.muni.cz"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. vladimir.horsky@mail.muni.cz","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. vladimir.horsky@mail.muni.cz","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122624986","display_name":"Radka Svobodov\u00e1","orcid":null},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"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":"Radka Svobodov\u00e1","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. radka.svobodova@mail.muni.cz","National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. radka.svobodova@mail.muni.cz"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. radka.svobodova@mail.muni.cz","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. radka.svobodova@mail.muni.cz","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058084999","display_name":"Ond\u0159ej Schindler","orcid":"https://orcid.org/0000-0002-9047-0334"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"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":true,"raw_author_name":"Ond\u0159ej Schindler","raw_affiliation_strings":["CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. ondrej.schindler@mail.muni.cz","National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. ondrej.schindler@mail.muni.cz"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. ondrej.schindler@mail.muni.cz","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic. ondrej.schindler@mail.muni.cz","institution_ids":["https://openalex.org/I21449261"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5058084999"],"corresponding_institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I21449261"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":3.6177,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.85801223,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":97},"biblio":{"volume":"18","issue":"1","first_page":"17","last_page":"17"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.454800009727478,"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":0.454800009727478,"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":0.13510000705718994,"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":0.10840000212192535,"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/cyclopentane","display_name":"Cyclopentane","score":0.8148999810218811},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8070999979972839},{"id":"https://openalex.org/keywords/ring","display_name":"Ring (chemistry)","score":0.8048999905586243},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.7389000058174133},{"id":"https://openalex.org/keywords/cyclohexane","display_name":"Cyclohexane","score":0.6682999730110168},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.6226000189781189},{"id":"https://openalex.org/keywords/benzene","display_name":"Benzene","score":0.5254999995231628}],"concepts":[{"id":"https://openalex.org/C2778556512","wikidata":"https://www.wikidata.org/wiki/Q80260","display_name":"Cyclopentane","level":2,"score":0.8148999810218811},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8070999979972839},{"id":"https://openalex.org/C2780378348","wikidata":"https://www.wikidata.org/wiki/Q25351438","display_name":"Ring (chemistry)","level":2,"score":0.8048999905586243},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.7389000058174133},{"id":"https://openalex.org/C2778237882","wikidata":"https://www.wikidata.org/wiki/Q211433","display_name":"Cyclohexane","level":2,"score":0.6682999730110168},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.6226000189781189},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5342000126838684},{"id":"https://openalex.org/C2777691172","wikidata":"https://www.wikidata.org/wiki/Q2270","display_name":"Benzene","level":2,"score":0.5254999995231628},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4909999966621399},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.38179999589920044},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3783000111579895},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3750999867916107},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3553999960422516},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.30959999561309814},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.3075999915599823},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.30149999260902405},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3010999858379364},{"id":"https://openalex.org/C2779200411","wikidata":"https://www.wikidata.org/wiki/Q80250","display_name":"Cyclopropane","level":3,"score":0.29840001463890076},{"id":"https://openalex.org/C6652555","wikidata":"https://www.wikidata.org/wiki/Q3285479","display_name":"Cyclohexane conformation","level":4,"score":0.26840001344680786},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.2583000063896179},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2565999925136566},{"id":"https://openalex.org/C2989255885","wikidata":"https://www.wikidata.org/wiki/Q500256","display_name":"Molecular conformation","level":3,"score":0.2556000053882599}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13321-026-01154-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01154-0","pdf_url":null,"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:41519762","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41519762","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:doaj.org/article:f25c697e4f7e4ed48da22fd9f7e16c4c","is_oa":true,"landing_page_url":"https://doaj.org/article/f25c697e4f7e4ed48da22fd9f7e16c4c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 18, Iss 1, Pp 1-15 (2026)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11689648","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12882122","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:2553903","is_oa":true,"landing_page_url":"https://is.muni.cz/publication/2553903","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12882122","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12882122/","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 Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-026-01154-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01154-0","pdf_url":null,"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":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1516459493","https://openalex.org/W1553810884","https://openalex.org/W1630585365","https://openalex.org/W1982414593","https://openalex.org/W1986134153","https://openalex.org/W1995808589","https://openalex.org/W2002524971","https://openalex.org/W2016021369","https://openalex.org/W2025511857","https://openalex.org/W2057668415","https://openalex.org/W2066860021","https://openalex.org/W2067718414","https://openalex.org/W2077467665","https://openalex.org/W2084761690","https://openalex.org/W2087212232","https://openalex.org/W2088178727","https://openalex.org/W2095461786","https://openalex.org/W2098260269","https://openalex.org/W2111136103","https://openalex.org/W2154714625","https://openalex.org/W2157728484","https://openalex.org/W2163910647","https://openalex.org/W2170163394","https://openalex.org/W2176969324","https://openalex.org/W2314327218","https://openalex.org/W2315820203","https://openalex.org/W2318304331","https://openalex.org/W2586302636","https://openalex.org/W2601470090","https://openalex.org/W2754938970","https://openalex.org/W2771627141","https://openalex.org/W2789465560","https://openalex.org/W2790159834","https://openalex.org/W2952578765","https://openalex.org/W2955375962","https://openalex.org/W2982977147","https://openalex.org/W3005123759","https://openalex.org/W3035930168","https://openalex.org/W3157649867","https://openalex.org/W3159719254","https://openalex.org/W3191346466","https://openalex.org/W4229042017","https://openalex.org/W4246085118","https://openalex.org/W4281977447","https://openalex.org/W4295779282","https://openalex.org/W4378364213","https://openalex.org/W6964002049","https://openalex.org/W7133228273"],"related_works":[],"abstract_inverted_index":{"Protein":[0,87],"structural":[1],"data":[2],"are":[3,78,218,264],"highly":[4],"valuable":[5],"for":[6,35,43,186,206,289,300],"research,":[7],"and":[8,39,48,66,90,129,165,183,239,257,292],"many":[9],"significant":[10],"results":[11],"have":[12],"been":[13],"published":[14],"on":[15],"their":[16,25,46,226],"basis.":[17],"An":[18],"important":[19],"part":[20],"of":[21,29,63,80,114,156,199,235,254,266,285],"protein":[22,82,237,268],"structures":[23,83,138,150,161,168,178,269],"is":[24,33,117,279],"ligands.":[26,144],"The":[27,69,112],"conformation":[28],"rings":[30,73],"in":[31,85,181,261,271,308],"ligands":[32,185],"crucial":[34],"the":[36,49,86,100,115,130,197,211,233,236,241,272,281,286],"ligands'":[37],"scaffold":[38],"shape":[40],"and,":[41],"therefore,":[42],"interactions":[44],"with":[45],"surroundings":[47],"subsequent":[50],"biological":[51],"function.":[52],"For":[53],"this":[54],"reason,":[55],"we":[56,296],"developed":[57],"a":[58,251],"workflow":[59,70,98,116,131],"to":[60,103,195,231],"detect":[61],"conformations":[62,217],"cyclohexane,":[64,255,290],"cyclopentane,":[65,256,291],"benzene":[67,166,258,293],"rings.":[68,294],"can":[71,179,192,203,305],"process":[72],"originating":[74,139],"from":[75,140],"ligands,":[76,201,262],"which":[77,124,202,263,304],"parts":[79,265],"experimental":[81,245,267],"deposited":[84,270],"Data":[88],"Bank":[89],"determined":[91],"by":[92,119,221],"X-ray":[93],"crystallography.":[94],"This":[95,274],"fully":[96],"automatic":[97,126],"utilises":[99],"Hill-Reilly":[101,287,298],"approach":[102,288],"calculate":[104],"puckering":[105],"angles":[106],"that":[107,147,174],"quantitatively":[108],"describe":[109],"ring":[110,137,149,160,167,177,216,302],"conformation.":[111],"reproducibility":[113],"guaranteed":[118],"storing":[120],"datasets":[121],"within":[122],"Onedata,":[123],"enables":[125],"dataset":[127],"retrieval":[128],"execution.":[132],"We":[133,145,172],"analysed":[134],"128":[135],"012":[136],"25":[141],"479":[142],"different":[143],"found":[146],"cyclohexane":[148,182],"include":[151],"more":[152],"than":[153],"22":[154],"%":[155,164],"unfavourable":[157,176,215],"conformations,":[158,303],"cyclopentane":[159,184],"about":[162],"5":[163],"only":[169],"0.01":[170],"%.":[171],"discovered":[173],"energetically":[175,214],"occur":[180],"proper":[187],"chemical":[188],"reasons.":[189],"Their":[190],"examination":[191],"help":[193],"us":[194],"understand":[196],"binding":[198],"these":[200,301],"be":[204,306],"helpful":[205],"pharmacology,":[207],"chemoinformatics,":[208],"etc.":[209],"On":[210],"other":[212,276,309],"hand,":[213],"often":[219],"caused":[220],"model":[222,238],"quality":[223,234],"issues.":[224],"Therefore,":[225],"occurrence":[227],"should":[228],"motivate":[229],"researchers":[230],"inspect":[232],"also":[240],"ring's":[242],"fit":[243],"into":[244],"data.Scientific":[246],"Contribution:":[247],"Our":[248],"analysis":[249],"uncovers":[250],"conformational":[252],"behaviour":[253],"rings,":[259],"occurring":[260],"PDB.":[273],"paper's":[275],"substantial":[277],"contribution":[278],"presenting":[280],"first":[282],"successful":[283],"application":[284],"Moreover,":[295],"provide":[297],"parameters":[299],"used":[307],"analyses.":[310]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2026-01-10T00:00:00"}
