{"id":"https://openalex.org/W4385514473","doi":"https://doi.org/10.1007/s10822-023-00524-2","title":"Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design","display_name":"Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design","publication_year":2023,"publication_date":"2023-08-03","ids":{"openalex":"https://openalex.org/W4385514473","doi":"https://doi.org/10.1007/s10822-023-00524-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/37535171"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-023-00524-2","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1007/s10822-023-00524-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-023-00524-2.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10822-023-00524-2.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005430934","display_name":"Ajay N. Jain","orcid":"https://orcid.org/0000-0003-4641-8501"},"institutions":[{"id":"https://openalex.org/I4210091371","display_name":"Fort Ross Conservancy","ror":"https://ror.org/00fpr8c10","country_code":"US","type":"other","lineage":["https://openalex.org/I4210091371"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ajay N. Jain","raw_affiliation_strings":["Research and Development, BioPharmics LLC, Sonoma County, CA, USA. ajain@jainlab.org","Research and Development, BioPharmics LLC, Sonoma County, CA, USA"],"raw_orcid":"https://orcid.org/0000-0003-4641-8501","affiliations":[{"raw_affiliation_string":"Research and Development, BioPharmics LLC, Sonoma County, CA, USA. ajain@jainlab.org","institution_ids":["https://openalex.org/I4210091371"]},{"raw_affiliation_string":"Research and Development, BioPharmics LLC, Sonoma County, CA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007691397","display_name":"Alexander C. Brueckner","orcid":"https://orcid.org/0000-0001-5866-0878"},"institutions":[{"id":"https://openalex.org/I4210091812","display_name":"Bristol-Myers Squibb (United States)","ror":"https://ror.org/00gtmwv55","country_code":"US","type":"company","lineage":["https://openalex.org/I4210091812"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander C. Brueckner","raw_affiliation_strings":["Bristol-Myers Squibb Company, Princeton, NJ, USA"],"raw_orcid":"https://orcid.org/0000-0001-5866-0878","affiliations":[{"raw_affiliation_string":"Bristol-Myers Squibb Company, Princeton, NJ, USA","institution_ids":["https://openalex.org/I4210091812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086555326","display_name":"Christine Jorge","orcid":"https://orcid.org/0009-0008-0536-9727"},"institutions":[{"id":"https://openalex.org/I4210091812","display_name":"Bristol-Myers Squibb (United States)","ror":"https://ror.org/00gtmwv55","country_code":"US","type":"company","lineage":["https://openalex.org/I4210091812"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christine Jorge","raw_affiliation_strings":["Bristol-Myers Squibb Company, Princeton, NJ, USA"],"raw_orcid":"https://orcid.org/0009-0008-0536-9727","affiliations":[{"raw_affiliation_string":"Bristol-Myers Squibb Company, Princeton, NJ, USA","institution_ids":["https://openalex.org/I4210091812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014710862","display_name":"Ann E. Cleves","orcid":"https://orcid.org/0000-0002-1622-2770"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ann E. Cleves","raw_affiliation_strings":["Research and Development, BioPharmics LLC, Sonoma County, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-1622-2770","affiliations":[{"raw_affiliation_string":"Research and Development, BioPharmics LLC, Sonoma County, CA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025914970","display_name":"Purnima Khandelwal","orcid":null},"institutions":[{"id":"https://openalex.org/I4210091812","display_name":"Bristol-Myers Squibb (United States)","ror":"https://ror.org/00gtmwv55","country_code":"US","type":"company","lineage":["https://openalex.org/I4210091812"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Purnima Khandelwal","raw_affiliation_strings":["Bristol-Myers Squibb Company, Princeton, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bristol-Myers Squibb Company, Princeton, NJ, USA","institution_ids":["https://openalex.org/I4210091812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047909184","display_name":"Janet Caceres\u2010Cortes","orcid":"https://orcid.org/0000-0002-0944-8843"},"institutions":[{"id":"https://openalex.org/I4210091812","display_name":"Bristol-Myers Squibb (United States)","ror":"https://ror.org/00gtmwv55","country_code":"US","type":"company","lineage":["https://openalex.org/I4210091812"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Janet Caceres Cortes","raw_affiliation_strings":["Bristol-Myers Squibb Company, Princeton, NJ, USA"],"raw_orcid":"https://orcid.org/0000-0002-0944-8843","affiliations":[{"raw_affiliation_string":"Bristol-Myers Squibb Company, Princeton, NJ, USA","institution_ids":["https://openalex.org/I4210091812"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005673469","display_name":"Luciano Mueller","orcid":"https://orcid.org/0000-0002-8956-2653"},"institutions":[{"id":"https://openalex.org/I157075465","display_name":"Bristol-Myers Squibb (Germany)","ror":"https://ror.org/032hfv632","country_code":"DE","type":"company","lineage":["https://openalex.org/I157075465","https://openalex.org/I4210091812"]},{"id":"https://openalex.org/I4210091812","display_name":"Bristol-Myers Squibb (United States)","ror":"https://ror.org/00gtmwv55","country_code":"US","type":"company","lineage":["https://openalex.org/I4210091812"]},{"id":"https://openalex.org/I4210134011","display_name":"Bristol-Myers Squibb (Sweden)","ror":"https://ror.org/035hx4w46","country_code":"SE","type":"company","lineage":["https://openalex.org/I4210091812","https://openalex.org/I4210134011"]}],"countries":["DE","SE","US"],"is_corresponding":false,"raw_author_name":"Luciano Mueller","raw_affiliation_strings":["Bristol-Myers Squibb Company, Princeton, NJ, USA. luciano.mueller@bms.com","Bristol-Myers Squibb Company, Princeton, NJ, USA"],"raw_orcid":"https://orcid.org/0000-0002-8956-2653","affiliations":[{"raw_affiliation_string":"Bristol-Myers Squibb Company, Princeton, NJ, USA. luciano.mueller@bms.com","institution_ids":["https://openalex.org/I4210134011","https://openalex.org/I157075465"]},{"raw_affiliation_string":"Bristol-Myers Squibb Company, Princeton, NJ, USA","institution_ids":["https://openalex.org/I4210091812"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5005430934"],"corresponding_institution_ids":["https://openalex.org/I4210091371"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":{"value":2890,"currency":"EUR","value_usd":3690},"fwci":1.1996,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.79197949,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"37","issue":"11","first_page":"519","last_page":"535"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9994000196456909,"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"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","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"}}],"keywords":[{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.624864399433136},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6247103810310364},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5297430753707886},{"id":"https://openalex.org/keywords/intermolecular-force","display_name":"Intermolecular force","score":0.516075074672699},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4603021740913391},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4439539909362793},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4395871162414551},{"id":"https://openalex.org/keywords/maxima-and-minima","display_name":"Maxima and minima","score":0.4171975255012512},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3623068332672119},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.25046244263648987},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.0950666069984436},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07405582070350647},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.06467154622077942}],"concepts":[{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.624864399433136},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6247103810310364},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5297430753707886},{"id":"https://openalex.org/C166950319","wikidata":"https://www.wikidata.org/wiki/Q245031","display_name":"Intermolecular force","level":3,"score":0.516075074672699},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4603021740913391},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4439539909362793},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4395871162414551},{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.4171975255012512},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3623068332672119},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.25046244263648987},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0950666069984436},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07405582070350647},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.06467154622077942},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012189","descriptor_name":"Retrospective Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1007/s10822-023-00524-2","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1007/s10822-023-00524-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-023-00524-2.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:37535171","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37535171","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 computer-aided molecular design","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10505130","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10505130","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10505130/pdf/10822_2023_Article_524.pdf","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 Comput Aided Mol Des","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s10822-023-00524-2","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1007/s10822-023-00524-2","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-023-00524-2.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Computer-Aided Molecular Design","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7799999713897705,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385514473.pdf"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W885225496","https://openalex.org/W1532848864","https://openalex.org/W1969164033","https://openalex.org/W1972459558","https://openalex.org/W1988219803","https://openalex.org/W2000948557","https://openalex.org/W2016098772","https://openalex.org/W2017139828","https://openalex.org/W2021001692","https://openalex.org/W2026692111","https://openalex.org/W2044038786","https://openalex.org/W2069344005","https://openalex.org/W2076755375","https://openalex.org/W2077467665","https://openalex.org/W2078145018","https://openalex.org/W2091572890","https://openalex.org/W2098060208","https://openalex.org/W2102686696","https://openalex.org/W2114296842","https://openalex.org/W2136332525","https://openalex.org/W2166813325","https://openalex.org/W2331896219","https://openalex.org/W2596982648","https://openalex.org/W2739232261","https://openalex.org/W2942963152","https://openalex.org/W2981618201","https://openalex.org/W3048848973","https://openalex.org/W3082180988","https://openalex.org/W3115932690","https://openalex.org/W3132756803","https://openalex.org/W3136989458","https://openalex.org/W3164288614","https://openalex.org/W3196622003","https://openalex.org/W4231031051","https://openalex.org/W4281686218","https://openalex.org/W4283792334","https://openalex.org/W4318142102"],"related_works":["https://openalex.org/W2375684291","https://openalex.org/W2354676191","https://openalex.org/W3188646203","https://openalex.org/W2909957174","https://openalex.org/W136674370","https://openalex.org/W4246278799","https://openalex.org/W2105527480","https://openalex.org/W2052387497","https://openalex.org/W2050203848","https://openalex.org/W2050191802"],"abstract_inverted_index":{"Systematic":[0],"optimization":[1,99,179],"of":[2,26,52,159],"large":[3,135],"macrocyclic":[4,150],"peptide":[5],"ligands":[6],"is":[7,153],"a":[8,23,53,189],"serious":[9],"challenge.":[10],"Here,":[11],"we":[12],"describe":[13,90],"an":[14,91],"approach":[15,94,191],"for":[16,65,111,168,174,180],"lead-optimization":[17],"using":[18,188],"the":[19,157],"PD-1/PD-L1":[20],"system":[21],"as":[22],"retrospective":[24],"example":[25],"moving":[27],"from":[28],"initial":[29],"lead":[30,54,133],"compound":[31],"to":[32,47,61,69,100,108,134],"clinical":[33],"candidate.":[34],"We":[35,88],"show":[36],"how":[37],"conformational":[38,63,151],"restraints":[39,57],"can":[40,58,183],"be":[41,59,109,184],"derived":[42],"by":[43],"exploiting":[44],"NMR":[45],"data":[46,195],"identify":[48],"low-energy":[49],"solution":[50],"ensembles":[51],"compound.":[55],"Such":[56],"used":[60],"focus":[62],"search":[64,152,173],"analogs":[66],"in":[67,137,156],"order":[68],"accurately":[70],"predict":[71,101],"bound":[72,102,127],"ligand":[73,81,118,163],"poses":[74],"through":[75],"molecular":[76,97],"docking":[77],"and":[78,83,198],"thereby":[79],"estimate":[80],"strain":[82,139],"protein-ligand":[84],"intermolecular":[85,130],"binding":[86,146],"energy.":[87],"also":[89],"analogous":[92],"ligand-based":[93],"that":[95,140,192],"employs":[96],"similarity":[98],"poses.":[103],"Both":[104],"approaches":[105],"are":[106],"shown":[107],"effective":[110],"prioritizing":[112],"lead-compound":[113],"analogs.":[114],"Surprisingly,":[115],"relatively":[116],"small":[117],"modifications,":[119],"which":[120],"may":[121],"have":[122,141],"minimal":[123],"effects":[124,143],"on":[125,144],"predicted":[126],"pose":[128],"or":[129,171],"interactions,":[131],"often":[132],"changes":[136],"estimated":[138],"dominating":[142],"overall":[145],"energy":[147],"estimates.":[148],"Effective":[149],"crucial,":[154],"whether":[155],"context":[158],"NMR-based":[160],"restraints,":[161],"X-ray":[162],"refinement,":[164],"partial":[165],"torsional":[166],"restraint":[167],"docking/ligand-similarity":[169],"calculations":[170],"agnostic":[172],"nominal":[175],"global":[176],"minima.":[177],"Lead":[178],"peptidic":[181],"macrocycles":[182],"made":[185],"more":[186],"productive":[187],"multi-disciplinary":[190],"combines":[193],"biophysical":[194],"with":[196],"practical":[197],"efficient":[199],"computational":[200],"methods.":[201]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":7}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
