{"id":"https://openalex.org/W4409571670","doi":"https://doi.org/10.1186/s13321-025-00977-7","title":"The pucke.rs toolkit to facilitate sampling the conformational space of biomolecular monomers","display_name":"The pucke.rs toolkit to facilitate sampling the conformational space of biomolecular monomers","publication_year":2025,"publication_date":"2025-04-17","ids":{"openalex":"https://openalex.org/W4409571670","doi":"https://doi.org/10.1186/s13321-025-00977-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/40247410"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-00977-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00977-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00977-7","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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/s13321-025-00977-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082185852","display_name":"J\u00e9r\u00f4me Rihon","orcid":"https://orcid.org/0000-0002-9207-1556"},"institutions":[{"id":"https://openalex.org/I24156275","display_name":"Rega Institute for Medical Research","ror":"https://ror.org/03w5j8p12","country_code":"BE","type":"facility","lineage":["https://openalex.org/I24156275"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"J\u00e9r\u00f4me Rihon","raw_affiliation_strings":["Laboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium"],"affiliations":[{"raw_affiliation_string":"Laboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium","institution_ids":["https://openalex.org/I24156275"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115547155","display_name":"Sten Reynders","orcid":"https://orcid.org/0000-0002-3819-722X"},"institutions":[{"id":"https://openalex.org/I24156275","display_name":"Rega Institute for Medical Research","ror":"https://ror.org/03w5j8p12","country_code":"BE","type":"facility","lineage":["https://openalex.org/I24156275"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Sten Reynders","raw_affiliation_strings":["Laboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium"],"affiliations":[{"raw_affiliation_string":"Laboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium","institution_ids":["https://openalex.org/I24156275"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064588864","display_name":"Vitor B. Pinheiro","orcid":"https://orcid.org/0000-0003-2491-0028"},"institutions":[{"id":"https://openalex.org/I24156275","display_name":"Rega Institute for Medical Research","ror":"https://ror.org/03w5j8p12","country_code":"BE","type":"facility","lineage":["https://openalex.org/I24156275"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Vitor Bernardes Pinheiro","raw_affiliation_strings":["Laboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium"],"affiliations":[{"raw_affiliation_string":"Laboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium","institution_ids":["https://openalex.org/I24156275"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051638010","display_name":"Eveline Lescrinier","orcid":"https://orcid.org/0000-0001-7066-4329"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eveline Lescrinier","raw_affiliation_strings":["Laboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium. eveline.lescrinier@kuleuven.be"],"affiliations":[{"raw_affiliation_string":"Laboratory of Medicinal Chemistry, Departement of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium. eveline.lescrinier@kuleuven.be","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5082185852"],"corresponding_institution_ids":["https://openalex.org/I24156275"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06715059,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"1","first_page":"53","last_page":"53"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9988999962806702,"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":0.9988999962806702,"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/T11162","display_name":"Enzyme Structure and Function","score":0.998199999332428,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9977999925613403,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.628946840763092},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.5566766262054443},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.47751370072364807},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4655841886997223},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4140644967556},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34825068712234497},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.33097317814826965},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1217045783996582},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.0733538568019867}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.628946840763092},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.5566766262054443},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.47751370072364807},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4655841886997223},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4140644967556},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34825068712234497},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33097317814826965},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1217045783996582},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0733538568019867},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13321-025-00977-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00977-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00977-7","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:40247410","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40247410","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:lirias2repo.kuleuven.be:20.500.12942/769522","is_oa":false,"landing_page_url":"https://lirias.kuleuven.be/handle/20.500.12942/769522","pdf_url":null,"source":{"id":"https://openalex.org/S4306401954","display_name":"Lirias (KU Leuven)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99464096","host_organization_name":"KU Leuven","host_organization_lineage":["https://openalex.org/I99464096"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Journal Of Cheminformatics, vol. 17 (1), Art.No. 53","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:doaj.org/article:6dc20cc8e3ef476990e7a47aaea8c3aa","is_oa":true,"landing_page_url":"https://doaj.org/article/6dc20cc8e3ef476990e7a47aaea8c3aa","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-20 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12007234","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12007234","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-00977-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00977-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00977-7","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4409571670.pdf"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1966204340","https://openalex.org/W1971275758","https://openalex.org/W1981807278","https://openalex.org/W1982414593","https://openalex.org/W1990406970","https://openalex.org/W1998252402","https://openalex.org/W2008423326","https://openalex.org/W2020879467","https://openalex.org/W2045974535","https://openalex.org/W2048233935","https://openalex.org/W2049996223","https://openalex.org/W2051891162","https://openalex.org/W2061822610","https://openalex.org/W2076985575","https://openalex.org/W2080747029","https://openalex.org/W2081046982","https://openalex.org/W2087212232","https://openalex.org/W2092157292","https://openalex.org/W2092265729","https://openalex.org/W2096747776","https://openalex.org/W2119547517","https://openalex.org/W2122199548","https://openalex.org/W2132629607","https://openalex.org/W2136567909","https://openalex.org/W2136729627","https://openalex.org/W2145408306","https://openalex.org/W2324265905","https://openalex.org/W2344252179","https://openalex.org/W2585740628","https://openalex.org/W2735699805","https://openalex.org/W2737449748","https://openalex.org/W2936033307","https://openalex.org/W2952047419","https://openalex.org/W3034310241","https://openalex.org/W3163516560","https://openalex.org/W4214717205","https://openalex.org/W4252911439","https://openalex.org/W4313706607","https://openalex.org/W4323352404","https://openalex.org/W4367724375","https://openalex.org/W4384106249","https://openalex.org/W4387950610","https://openalex.org/W4392188374","https://openalex.org/W4406864968","https://openalex.org/W6968948892"],"related_works":["https://openalex.org/W2038693912","https://openalex.org/W1991602789","https://openalex.org/W1582396021","https://openalex.org/W2807783496","https://openalex.org/W2038905316","https://openalex.org/W2051452952","https://openalex.org/W2057866436","https://openalex.org/W1977155515","https://openalex.org/W2776417242","https://openalex.org/W1551441281"],"abstract_inverted_index":{"Understanding":[0],"of":[1,7,34,98,102,113],"the":[2,19,63,114],"structural":[3],"and":[4,57,107,123],"dynamic":[5],"behaviour":[6],"molecules":[8],"is":[9,22,116],"a":[10,32,53,58,86,91,95],"major":[11],"objective":[12],"in":[13],"molecular":[14],"modeling":[15],"research.":[16],"Sampling":[17],"through":[18],"torsional":[20],"space":[21],"an":[23],"efficient":[24],"way":[25],"to":[26,46,48,61,65,73,81,94],"map":[27],"their":[28],"behaviour.":[29],"However,":[30],"generating":[31],"landscape":[33],"possible":[35],"conformations":[36],"relies":[37],"on":[38,89,118],"multiple":[39],"formalisms":[40,75],"whose":[41],"mathematics":[42],"are":[43],"often":[44],"difficult":[45],"convert":[47],"code.":[49],"Here":[50],"we":[51,84],"present":[52],"command":[54],"line":[55],"tool":[56,115],"scripting":[59],"module":[60],"provide":[62],"means":[64],"generate":[66],"such":[67],"landscapes":[68],"with":[69],"different":[70],"axes":[71],"according":[72],"various":[74],"exploited":[76],"for":[77,104],"conformational":[78],"sampling.":[79],"Additionally":[80],"this":[82],"toolkit,":[83],"apply":[85],"benchmarking":[87],"study":[88],"subjecting":[90],"DNA":[92],"nucleoside":[93],"diverse":[96],"set":[97],"quantum":[99],"mechanical":[100],"levels":[101],"theory":[103],"geometry":[105],"optimisations":[106],"energy":[108],"potential":[109,112],"calculations.":[110],"The":[111],"demonstrated":[117],"examples":[119],"including":[120],"amino":[121],"acids":[122],"synthetic":[124],"nucleosides":[125],"having":[126],"five-membered":[127],"or":[128],"six-membered":[129],"sugar":[130],"moieties.":[131]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
