{"id":"https://openalex.org/W4403815133","doi":"https://doi.org/10.48550/arxiv.2409.20227","title":"Assessing interaction recovery of predicted protein-ligand poses","display_name":"Assessing interaction recovery of predicted protein-ligand poses","publication_year":2024,"publication_date":"2024-09-30","ids":{"openalex":"https://openalex.org/W4403815133","doi":"https://doi.org/10.48550/arxiv.2409.20227"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2409.20227","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2409.20227","pdf_url":"https://arxiv.org/pdf/2409.20227","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2409.20227","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076922592","display_name":"David Errington","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Errington, David","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091100763","display_name":"Constantin Schneider","orcid":"https://orcid.org/0000-0002-2579-0307"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Schneider, Constantin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036297733","display_name":"C\u00e9dric Bouysset","orcid":"https://orcid.org/0000-0002-7814-8158"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bouysset, C\u00e9dric","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5016534522","display_name":"Fr\u00e9d\u00e9ric A. Dreyer","orcid":"https://orcid.org/0000-0002-0445-7863"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dreyer, Fr\u00e9d\u00e9ric A.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9247999787330627,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9247999787330627,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/ligand","display_name":"Ligand (biochemistry)","score":0.5043052434921265},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3896715044975281},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.38567107915878296},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3856121003627777},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36485910415649414},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3011518716812134},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.16775453090667725},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.10686850547790527}],"concepts":[{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5043052434921265},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3896715044975281},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.38567107915878296},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3856121003627777},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36485910415649414},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3011518716812134},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.16775453090667725},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.10686850547790527}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2409.20227","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2409.20227","pdf_url":"https://arxiv.org/pdf/2409.20227","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2409.20227","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2409.20227","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2409.20227","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2409.20227","pdf_url":"https://arxiv.org/pdf/2409.20227","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403815133.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"The":[0],"field":[1],"of":[2,23,45,57,78],"protein-ligand":[3,32,71,85],"pose":[4,50],"prediction":[5],"has":[6],"seen":[7],"significant":[8],"advances":[9],"in":[10,21,83],"recent":[11,84],"years,":[12],"with":[13,61],"machine":[14],"learning-based":[15],"methods":[16,26],"now":[17],"being":[18],"commonly":[19],"used":[20],"lieu":[22],"classical":[24],"docking":[25],"or":[27],"even":[28],"to":[29,48,76,91],"predict":[30],"all-atom":[31],"complex":[33],"structures.":[34],"Most":[35],"contemporary":[36],"studies":[37],"focus":[38],"on":[39],"the":[40,58,62],"accuracy":[41],"and":[42],"physical":[43],"plausibility":[44],"ligand":[46],"placement":[47],"determine":[49],"quality,":[51],"often":[52,89],"neglecting":[53],"a":[54],"direct":[55],"assessment":[56],"interactions":[59],"observed":[60],"protein.":[63],"In":[64],"this":[65],"work,":[66],"we":[67],"demonstrate":[68],"that":[69],"ignoring":[70],"interaction":[72],"fingerprints":[73],"can":[74],"lead":[75],"overestimation":[77],"model":[79],"performance,":[80],"most":[81],"notably":[82],"cofolding":[86],"models":[87],"which":[88],"fail":[90],"recapitulate":[92],"key":[93],"interactions.":[94]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
