{"id":"https://openalex.org/W7221433017","doi":"https://doi.org/10.64898/2026.10.05.756260","title":"TopFor: Automated Preparation of AMBER-Compatible Parameters for Noncanonical Amino Acids in Peptides","display_name":"TopFor: Automated Preparation of AMBER-Compatible Parameters for Noncanonical Amino Acids in Peptides","publication_year":2026,"publication_date":"2026-10-11","ids":{"openalex":"https://openalex.org/W7221433017","doi":"https://doi.org/10.64898/2026.10.05.756260"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.05.756260","doi":"https://doi.org/10.64898/2026.10.05.756260","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.05.756260","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/11/2026.10.05.756260.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/11/2026.10.05.756260.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080402422","display_name":"Emre Fatih B\u00fclb\u00fcl","orcid":"https://orcid.org/0000-0002-9901-2022","observed_orcids":["https://orcid.org/0000-0002-9901-2022"]},"institutions":[{"id":"https://openalex.org/I4210124929","display_name":"Helmholtz Centre for Infection Research","ror":"https://ror.org/03d0p2685","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929"]},{"id":"https://openalex.org/I4210142777","display_name":"Helmholtz Institute for Pharmaceutical Research Saarland","ror":"https://ror.org/042dsac10","country_code":"DE","type":"government","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929","https://openalex.org/I4210142777"]},{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Emre F. B\u00fclb\u00fcl","raw_affiliation_strings":["Center for Bioinformatics, Saarland University, Campus E2.1, 66123, Saarbr\u00fccken, Germany","Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9901-2022","affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Saarland University, Campus E2.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I91712215"]},{"raw_affiliation_string":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210124929","https://openalex.org/I4210142777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5151785342","display_name":"Heshine Gnanasekar","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Heshine Gnanasekar","raw_affiliation_strings":["Center for Bioinformatics, Saarland University, Campus E2.1, 66123, Saarbr\u00fccken, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Saarland University, Campus E2.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I91712215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5158319457","display_name":"Carene Benasolo","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210124929","display_name":"Helmholtz Centre for Infection Research","ror":"https://ror.org/03d0p2685","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929"]},{"id":"https://openalex.org/I4210142777","display_name":"Helmholtz Institute for Pharmaceutical Research Saarland","ror":"https://ror.org/042dsac10","country_code":"DE","type":"government","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929","https://openalex.org/I4210142777"]},{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Car\u00e8ne A. Benasolo","raw_affiliation_strings":["Center for Bioinformatics, Saarland University, Campus E2.1, 66123, Saarbr\u00fccken, Germany","Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Saarland University, Campus E2.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I91712215"]},{"raw_affiliation_string":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210124929","https://openalex.org/I4210142777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051946384","display_name":"Sari Rasheed","orcid":"https://orcid.org/0000-0002-9700-0474","observed_orcids":["https://orcid.org/0000-0002-9700-0474"]},"institutions":[{"id":"https://openalex.org/I4210115305","display_name":"German Center for Infection Research","ror":"https://ror.org/028s4q594","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210115305","https://openalex.org/I4405256427"]},{"id":"https://openalex.org/I4210124929","display_name":"Helmholtz Centre for Infection Research","ror":"https://ror.org/03d0p2685","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929"]},{"id":"https://openalex.org/I4210142777","display_name":"Helmholtz Institute for Pharmaceutical Research Saarland","ror":"https://ror.org/042dsac10","country_code":"DE","type":"government","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929","https://openalex.org/I4210142777"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sari Rasheed","raw_affiliation_strings":["German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany","Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9700-0474","affiliations":[{"raw_affiliation_string":"German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany","institution_ids":["https://openalex.org/I4210115305"]},{"raw_affiliation_string":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210124929","https://openalex.org/I4210142777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077818118","display_name":"Rolf M\u00fcller","orcid":"https://orcid.org/0000-0002-1042-5665","observed_orcids":["https://orcid.org/0000-0002-1042-5665","https://orcid.org/0000-0001-6571-6630"]},"institutions":[{"id":"https://openalex.org/I4210115305","display_name":"German Center for Infection Research","ror":"https://ror.org/028s4q594","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210115305","https://openalex.org/I4405256427"]},{"id":"https://openalex.org/I4210124929","display_name":"Helmholtz Centre for Infection Research","ror":"https://ror.org/03d0p2685","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929"]},{"id":"https://openalex.org/I4210142777","display_name":"Helmholtz Institute for Pharmaceutical Research Saarland","ror":"https://ror.org/042dsac10","country_code":"DE","type":"government","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929","https://openalex.org/I4210142777"]},{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Rolf M\u00fcller","raw_affiliation_strings":["Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbr\u00fccken, Germany","German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany","Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany"],"raw_orcid":"https://orcid.org/0000-0002-1042-5665","affiliations":[{"raw_affiliation_string":"Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I91712215"]},{"raw_affiliation_string":"German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany","institution_ids":["https://openalex.org/I4210115305"]},{"raw_affiliation_string":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210124929","https://openalex.org/I4210142777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101632496","display_name":"Olga V. Kalinina","orcid":"https://orcid.org/0000-0002-9445-477X","observed_orcids":["https://orcid.org/0000-0002-9445-477X"]},"institutions":[{"id":"https://openalex.org/I4210124929","display_name":"Helmholtz Centre for Infection Research","ror":"https://ror.org/03d0p2685","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929"]},{"id":"https://openalex.org/I4210142777","display_name":"Helmholtz Institute for Pharmaceutical Research Saarland","ror":"https://ror.org/042dsac10","country_code":"DE","type":"government","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929","https://openalex.org/I4210142777"]},{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Olga V. Kalinina","raw_affiliation_strings":["Center for Bioinformatics, Saarland University, Campus E2.1, 66123, Saarbr\u00fccken, Germany","Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany","Medical Faculty, Saarland University, 66421, Homburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9445-477X","affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Saarland University, Campus E2.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I91712215"]},{"raw_affiliation_string":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210124929","https://openalex.org/I4210142777"]},{"raw_affiliation_string":"Medical Faculty, Saarland University, 66421, Homburg, Germany","institution_ids":["https://openalex.org/I91712215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075613196","display_name":"Kenan A. J. Bozh\u00fcy\u00fck","orcid":"https://orcid.org/0000-0002-8609-2967","observed_orcids":["https://orcid.org/0000-0002-8609-2967"]},"institutions":[{"id":"https://openalex.org/I4210124929","display_name":"Helmholtz Centre for Infection Research","ror":"https://ror.org/03d0p2685","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929"]},{"id":"https://openalex.org/I4210142777","display_name":"Helmholtz Institute for Pharmaceutical Research Saarland","ror":"https://ror.org/042dsac10","country_code":"DE","type":"government","lineage":["https://openalex.org/I1305996414","https://openalex.org/I4210124929","https://openalex.org/I4210142777"]},{"id":"https://openalex.org/I91712215","display_name":"Saarland University","ror":"https://ror.org/01jdpyv68","country_code":"DE","type":"education","lineage":["https://openalex.org/I91712215"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kenan A. J. Bozh\u00fcy\u00fck","raw_affiliation_strings":["Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbr\u00fccken, Germany","Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany","Myria Biosciences AG, Hochbergerstrasse 60C, 4057, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-8609-2967","affiliations":[{"raw_affiliation_string":"Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I91712215"]},{"raw_affiliation_string":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), PharmaScienceHub (PSH), Campus E8.1, 66123, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210124929","https://openalex.org/I4210142777"]},{"raw_affiliation_string":"Myria Biosciences AG, Hochbergerstrasse 60C, 4057, Basel, Switzerland","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.6079000234603882,"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":0.6079000234603882,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.3215000033378601,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.06080000102519989,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/unnatural-amino-acids","display_name":"unnatural amino acids","score":0.9850000143051147},{"id":"https://openalex.org/keywords/amber-force-field","display_name":"AMBER force field","score":0.7749999761581421},{"id":"https://openalex.org/keywords/topology-generation","display_name":"topology generation","score":0.5059999823570251},{"id":"https://openalex.org/keywords/cyclosporine","display_name":"cyclosporine","score":0.949999988079071},{"id":"https://openalex.org/keywords/dnan","display_name":"DNAN","score":0.5690000057220459},{"id":"https://openalex.org/keywords/mycobacterium-smegmatis","display_name":"Mycobacterium smegmatis","score":0.8330000042915344},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"virtual screening","score":0.3799999952316284}],"concepts":[{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.717199981212616},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.6901999711990356},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6435999870300293},{"id":"https://openalex.org/C168831097","wikidata":"https://www.wikidata.org/wiki/Q413248","display_name":"Depsipeptide","level":2,"score":0.6161999702453613},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5539000034332275},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5473999977111816},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.5343000292778015},{"id":"https://openalex.org/C60984968","wikidata":"https://www.wikidata.org/wiki/Q389172","display_name":"Cyclic peptide","level":3,"score":0.45339998602867126},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.43650001287460327},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.4077000021934509},{"id":"https://openalex.org/C2776923573","wikidata":"https://www.wikidata.org/wiki/Q2294884","display_name":"Derivatization","level":3,"score":0.38940000534057617},{"id":"https://openalex.org/C2994376932","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Amino acid residue","level":4,"score":0.38339999318122864},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3452000021934509},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33149999380111694},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3231000006198883},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.32269999384880066},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3091999888420105},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.30090001225471497},{"id":"https://openalex.org/C2779809887","wikidata":"https://www.wikidata.org/wiki/Q14864278","display_name":"Peptide synthesis","level":3,"score":0.3005000054836273},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.2856000065803528},{"id":"https://openalex.org/C124790011","wikidata":"https://www.wikidata.org/wiki/Q2069797","display_name":"Peptidomimetic","level":3,"score":0.2849000096321106},{"id":"https://openalex.org/C3019060180","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automated method","level":2,"score":0.27880001068115234},{"id":"https://openalex.org/C2776471321","wikidata":"https://www.wikidata.org/wiki/Q7166526","display_name":"Peptide library","level":4,"score":0.2721000015735626},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2599000036716461},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.25270000100135803}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.05.756260","doi":"https://doi.org/10.64898/2026.10.05.756260","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.05.756260","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/11/2026.10.05.756260.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.05.756260","doi":"https://doi.org/10.64898/2026.10.05.756260","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.05.756260","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/11/2026.10.05.756260.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7221433017.pdf","grobid_xml":"https://content.openalex.org/works/W7221433017.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W1504277857","https://openalex.org/W1827916032","https://openalex.org/W1966739973","https://openalex.org/W1968984443","https://openalex.org/W1976161355","https://openalex.org/W1976261939","https://openalex.org/W1994941561","https://openalex.org/W2008517160","https://openalex.org/W2011601475","https://openalex.org/W2015688756","https://openalex.org/W2021687697","https://openalex.org/W2030896354","https://openalex.org/W2035266068","https://openalex.org/W2037535298","https://openalex.org/W2050837608","https://openalex.org/W2066690664","https://openalex.org/W2067718414","https://openalex.org/W2070753604","https://openalex.org/W2072683434","https://openalex.org/W2106140689","https://openalex.org/W2109154308","https://openalex.org/W2132525235","https://openalex.org/W2144288821","https://openalex.org/W2313116527","https://openalex.org/W2332712348","https://openalex.org/W2404280981","https://openalex.org/W2602946330","https://openalex.org/W2793401118","https://openalex.org/W2889326414","https://openalex.org/W2911997094","https://openalex.org/W2923417513","https://openalex.org/W2989052455","https://openalex.org/W3086801715","https://openalex.org/W3127297964","https://openalex.org/W3161240351","https://openalex.org/W3196622003","https://openalex.org/W3197039015","https://openalex.org/W4212959738","https://openalex.org/W4294982900","https://openalex.org/W4307407988","https://openalex.org/W4321445531","https://openalex.org/W4366819307","https://openalex.org/W4378783128","https://openalex.org/W4387440676","https://openalex.org/W4387909502","https://openalex.org/W4388839879","https://openalex.org/W4391256275","https://openalex.org/W4393035403","https://openalex.org/W4396514592","https://openalex.org/W4402900883","https://openalex.org/W4405229058","https://openalex.org/W4406469811","https://openalex.org/W4407931905","https://openalex.org/W4409502001","https://openalex.org/W4410384688","https://openalex.org/W4412694289","https://openalex.org/W4415698405","https://openalex.org/W7138951421","https://openalex.org/W7161725630","https://openalex.org/W7169876729"],"related_works":["https://openalex.org/W7161725630","https://openalex.org/W4415698405","https://openalex.org/W7138951421","https://openalex.org/W7160949392","https://openalex.org/W7160845510","https://openalex.org/W2905381711","https://openalex.org/W4405229058","https://openalex.org/W2319394713","https://openalex.org/W6958589100","https://openalex.org/W7130531509"],"abstract_inverted_index":{"Abstract":[0],"Peptides":[1],"containing":[2],"noncanonical":[3],"amino":[4],"acids":[5],"(ncAAs)":[6],"are":[7],"becoming":[8],"increasingly":[9],"important":[10],"in":[11,97],"drug":[12],"discovery,":[13],"but":[14],"their":[15,218],"molecular":[16],"dynamics":[17],"(MD)":[18],"simulation":[19],"remains":[20],"limited":[21],"by":[22,80,89],"labor-intensive":[23],"residue":[24,49,84,105],"parameterization":[25,70,150],"and":[26,34,51,68,109,133,151,183,198,216,225],"topology":[27],"preparation.":[28],"Here,":[29],"we":[30],"present":[31],"TopFor":[32,64,90,149,162,203],"(Topology":[33],"Residue":[35],"Force-Field":[36],"Parameter":[37],"Preparation),":[38],"an":[39],"open-source,":[40],"peptide-oriented":[41],"workflow":[42,73,157,171],"that":[43],"automates":[44],"the":[45,77,114,127,134,152,174,205],"generation":[46],"of":[47,142,186],"ncAA":[48],"templates":[50],"force-field":[52],"parameter":[53],"files":[54],"for":[55,213],"MD":[56,102,214],"simulations":[57,215],"with":[58,86],"AMBER":[59,83,116],"using":[60,76,91,126],"established":[61],"charge-derivation":[62,93],"methods.":[63],"supports":[65],"single-residue,":[66],"whole-peptide,":[67],"batch":[69],"workflows.":[71,229],"The":[72],"was":[74,124,163],"validated":[75],"MDM2\u2013p53":[78],"complex":[79,121],"comparing":[81],"native":[82,115],"definitions":[85,106],"residues":[87],"processed":[88],"three":[92,98,199],"methods,":[94],"each":[95],"evaluated":[96],"independent":[99],"100":[100],"ns":[101],"simulations.":[103],"TopFor-generated":[104],"showed":[107,200],"structural":[108],"conformational":[110],"behavior":[111],"comparable":[112],"to":[113,119,209],"representation.":[117],"Applicability":[118],"more":[120],"peptide":[122,130,169,227],"architectures":[123],"demonstrated":[125],"head-to-tail":[128],"cyclic":[129,135],"cyclosporin":[131],"A":[132],"depsipeptide":[136],"cyclohexylgriselimycin.":[137],"At":[138],"library":[139],"scale,":[140],"1,138":[141],"1,214":[143],"cyclohexylgriselimycin":[144],"derivatives":[145],"(93.7%)":[146],"successfully":[147],"completed":[148],"subsequent":[153],"initial":[154],"AMBER-based":[155],"computational":[156,223],"across":[158],"two":[159],"derivatization":[160],"campaigns.":[161],"further":[164],"integrated":[165],"into":[166,220],"a":[167],"structure-based":[168,226],"discovery":[170,228],"based":[172],"on":[173],"DnaN\u2013griselimycin":[175],"complex.":[176],"Six":[177],"GM-derived":[178],"peptides":[179,212],"were":[180],"computationally":[181],"prioritized":[182],"experimentally":[184],"evaluated,":[185],"which":[187],"four":[188],"produced":[189],"SPR":[190],"responses":[191],"against":[192],"Mycobacterium":[193],"smegmatis":[194],"(M.":[195],"smegmatis)":[196],"DnaN":[197],"concentration-dependent":[201],"responses.":[202],"reduces":[204],"manual":[206],"effort":[207],"required":[208],"prepare":[210],"ncAA-containing":[211],"enables":[217],"integration":[219],"both":[221],"library-scale":[222],"screening":[224]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-10-12T00:00:00"}