{"id":"https://openalex.org/W91079099","doi":"https://doi.org/10.1186/1758-2946-5-s1-p3","title":"TorsionAnalyzer: exploring conformational space","display_name":"TorsionAnalyzer: exploring conformational space","publication_year":2013,"publication_date":"2013-03-01","ids":{"openalex":"https://openalex.org/W91079099","doi":"https://doi.org/10.1186/1758-2946-5-s1-p3","mag":"91079099"},"language":"de","primary_location":{"id":"doi:10.1186/1758-2946-5-s1-p3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-p3","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-P3","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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-P3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046206895","display_name":"Christin Sch\u00e4rfer","orcid":"https://orcid.org/0000-0002-2135-0777"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christin Sch\u00e4rfer","raw_affiliation_strings":["Center for Bioinformatics (ZBH), Bundesstr. 43, 20146, Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics (ZBH), Bundesstr. 43, 20146, Hamburg, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059481994","display_name":"Tanja Schulz\u2010Gasch","orcid":null},"institutions":[{"id":"https://openalex.org/I118019719","display_name":"Roche (Switzerland)","ror":"https://ror.org/00by1q217","country_code":"CH","type":"company","lineage":["https://openalex.org/I118019719"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Tanja Schulz-Gasch","raw_affiliation_strings":["F. Hoffmann-La Roche Ltd., 4070, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"F. Hoffmann-La Roche Ltd., 4070, Basel, Switzerland","institution_ids":["https://openalex.org/I118019719"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083205378","display_name":"Matthias Rarey","orcid":"https://orcid.org/0000-0002-9553-6531"},"institutions":[{"id":"https://openalex.org/I118019719","display_name":"Roche (Switzerland)","ror":"https://ror.org/00by1q217","country_code":"CH","type":"company","lineage":["https://openalex.org/I118019719"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["Center for Bioinformatics (ZBH), Bundesstr. 43, 20146, Hamburg, Germany","F. Hoffmann-La Roche Ltd., 4070, Basel, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics (ZBH), Bundesstr. 43, 20146, Hamburg, Germany","institution_ids":[]},{"raw_affiliation_string":"F. Hoffmann-La Roche Ltd., 4070, Basel, Switzerland","institution_ids":["https://openalex.org/I118019719"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.1496,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.54840315,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"5","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9984999895095825,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9980999827384949,"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/dihedral-angle","display_name":"Dihedral angle","score":0.7617781162261963},{"id":"https://openalex.org/keywords/torsion","display_name":"Torsion (gastropod)","score":0.7441443204879761},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6234057545661926},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5864731073379517},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5323142409324646},{"id":"https://openalex.org/keywords/histogram","display_name":"Histogram","score":0.4719369113445282},{"id":"https://openalex.org/keywords/molecular-conformation","display_name":"Molecular conformation","score":0.45534998178482056},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.44019851088523865},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.37978601455688477},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3470660448074341},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3292636573314667},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32355356216430664},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2903437912464142},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.26995494961738586},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.21489328145980835},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.19051027297973633},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.16202905774116516},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09733068943023682},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09025031328201294}],"concepts":[{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.7617781162261963},{"id":"https://openalex.org/C77461463","wikidata":"https://www.wikidata.org/wiki/Q7827201","display_name":"Torsion (gastropod)","level":2,"score":0.7441443204879761},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6234057545661926},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5864731073379517},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5323142409324646},{"id":"https://openalex.org/C53533937","wikidata":"https://www.wikidata.org/wiki/Q185020","display_name":"Histogram","level":3,"score":0.4719369113445282},{"id":"https://openalex.org/C2989255885","wikidata":"https://www.wikidata.org/wiki/Q500256","display_name":"Molecular conformation","level":3,"score":0.45534998178482056},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.44019851088523865},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.37978601455688477},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3470660448074341},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3292636573314667},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32355356216430664},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2903437912464142},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26995494961738586},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.21489328145980835},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.19051027297973633},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.16202905774116516},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09733068943023682},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09025031328201294},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","level":1,"score":0.0},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/1758-2946-5-s1-p3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-p3","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-P3","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":"pmh:oai:europepmc.org:2605499","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3606252","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-s1-p3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-s1-p3","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-S1-P3","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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W91079099.pdf","grobid_xml":"https://content.openalex.org/works/W91079099.grobid-xml"},"referenced_works_count":2,"referenced_works":["https://openalex.org/W2032842297","https://openalex.org/W2130479394"],"related_works":["https://openalex.org/W2128884622","https://openalex.org/W2112380088","https://openalex.org/W2059608951","https://openalex.org/W4384153500","https://openalex.org/W2021330892","https://openalex.org/W4387012733","https://openalex.org/W2951365081","https://openalex.org/W4252058432","https://openalex.org/W2044134997","https://openalex.org/W3008488198"],"abstract_inverted_index":{"Molecular":[0],"conformations":[1],"are":[2,120],"used":[3],"in":[4],"a":[5,18,26,35,48,62,82,102,118,150],"wide":[6],"range":[7],"of":[8,17,32,42,65,75,104,117,136,154,158,164,172,184,187,192],"virtual":[9],"screening":[10],"applications":[11],"to":[12,70,123,147],"represent":[13],"the":[14,21,30,39,72,112,134,140,145,155,165,173,180],"conformational":[15,23,40],"flexibility":[16],"molecule.":[19],"As":[20],"underlying":[22],"model":[24],"has":[25],"major":[27],"influence":[28],"on":[29],"results":[31],"these":[33],"applications,":[34],"closer":[36],"insight":[37],"into":[38,126],"space":[41],"molecules":[43],"is":[44,86,162],"very":[45],"important.\r\n\r\nWe":[46],"developed":[47],"new":[49],"interactive":[50],"graphical":[51],"software":[52],"tool":[53,60],"for":[54,189],"conformation":[55,119,161],"analysis":[56],"called":[57],"TorsionAnalyzer.":[58],"The":[59,167],"uses":[61],"predefined":[63],"set":[64],"over":[66],"450":[67],"SMARTS":[68,175],"patterns":[69,176,188],"analyze":[71],"torsion":[73,83,106,113,131,156],"angles":[74,107,138,157],"an":[76,159],"input":[77],"conformation.":[78],"Each":[79],"pattern":[80,101],"describes":[81],"angle":[84],"and":[85,95,129,182],"associated":[87],"with":[88],"frequency":[89],"histograms":[90],"derived":[91,110],"from":[92,111,139],"CSD":[93],"[1]":[94],"PDB":[96],"[2]":[97],"data.":[98],"For":[99],"each":[100],"list":[103,135],"allowed":[105,137],"was":[108],"automatically":[109],"histograms.":[114],"Rotatable":[115],"bonds":[116],"colored":[121],"according":[122],"their":[124],"classification":[125],"usual,":[127],"borderline":[128],"unusual":[130],"angles,":[132],"using":[133],"corresponding":[141],"patterns.":[142],"This":[143],"allows":[144],"user":[146],"see":[148],"at":[149],"glance":[151],"if":[152],"one":[153],"examined":[160],"out":[163],"ordinary.":[166],"TorsionAnalyzer":[168],"supports":[169],"easy":[170],"modification":[171],"existing":[174],"as":[177,179],"well":[178],"preparation":[181],"storage":[183],"different":[185,190],"sets":[186,191],"molecules.":[193]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}