{"id":"https://openalex.org/W4313454189","doi":"https://doi.org/10.1021/acs.jcim.2c00945","title":"LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling","display_name":"LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling","publication_year":2023,"publication_date":"2023-01-03","ids":{"openalex":"https://openalex.org/W4313454189","doi":"https://doi.org/10.1021/acs.jcim.2c00945","pmid":"https://pubmed.ncbi.nlm.nih.gov/36594886"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00945","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00945","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://escholarship.org/content/qt6j2330sq/qt6j2330sq.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051935828","display_name":"Reecan J. Juarez","orcid":"https://orcid.org/0000-0003-3307-1617"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Reecan J. Juarez","raw_affiliation_strings":["Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37235, United States"],"affiliations":[{"raw_affiliation_string":"Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37235, United States","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004417541","display_name":"Yaoyukun Jiang","orcid":"https://orcid.org/0000-0002-6424-2231"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yaoyukun Jiang","raw_affiliation_strings":["Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028783884","display_name":"Matthew Tremblay","orcid":"https://orcid.org/0000-0001-6378-2685"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Tremblay","raw_affiliation_strings":["Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059001674","display_name":"Qianzhen Shao","orcid":"https://orcid.org/0000-0002-7787-0966"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qianzhen Shao","raw_affiliation_strings":["Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005422184","display_name":"A. James Link","orcid":"https://orcid.org/0000-0001-5066-9691"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. James Link","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Chemistry and Molecular Biology, Princeton University, 207 Hoyt Laboratory, Princeton, New Jersey 08544, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Chemistry and Molecular Biology, Princeton University, 207 Hoyt Laboratory, Princeton, New Jersey 08544, United States","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055785990","display_name":"Zhongyue Yang","orcid":"https://orcid.org/0000-0003-0395-6617"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhongyue J. Yang","raw_affiliation_strings":["Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States","Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States","Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States","Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States","Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States"],"affiliations":[{"raw_affiliation_string":"Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5055785990"],"corresponding_institution_ids":["https://openalex.org/I200719446"],"apc_list":null,"apc_paid":null,"fwci":4.3899,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.94984427,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"63","issue":"2","first_page":"522","last_page":"530"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","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"}},{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","score":0.9976999759674072,"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/lasso","display_name":"Lasso (programming language)","score":0.7037612199783325},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.6750941276550293},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.48622003197669983},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46399518847465515},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.44215330481529236},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.43161529302597046},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4043700695037842},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37306225299835205},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.36335211992263794},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.32255351543426514},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.194065123796463},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15046590566635132},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.13963797688484192},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1283133327960968}],"concepts":[{"id":"https://openalex.org/C37616216","wikidata":"https://www.wikidata.org/wiki/Q3218363","display_name":"Lasso (programming language)","level":2,"score":0.7037612199783325},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.6750941276550293},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.48622003197669983},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46399518847465515},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.44215330481529236},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.43161529302597046},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4043700695037842},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37306225299835205},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.36335211992263794},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32255351543426514},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.194065123796463},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15046590566635132},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.13963797688484192},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1283133327960968},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.2c00945","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00945","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:36594886","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36594886","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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt6j2330sq","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/6j2330sq","pdf_url":"https://escholarship.org/content/qt6j2330sq/qt6j2330sq.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, vol 63, iss 2","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10117200","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10117200","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10117200/pdf/nihms-1878453.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:escholarship.org:ark:/13030/qt6j2330sq","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/6j2330sq","pdf_url":"https://escholarship.org/content/qt6j2330sq/qt6j2330sq.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, vol 63, iss 2","raw_type":"article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1144917124","display_name":null,"funder_award_id":"T32 GM00832","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1508757563","display_name":null,"funder_award_id":"GM107036","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2191040125","display_name":null,"funder_award_id":"FF_300061.10","funder_id":"https://openalex.org/F4320333026","funder_display_name":"Department of Chemistry, Vanderbilt University"},{"id":"https://openalex.org/G3013808599","display_name":null,"funder_award_id":"GM107036","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3288751766","display_name":null,"funder_award_id":"T32 GM008320","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3718023403","display_name":null,"funder_award_id":"BIO200057","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G417905534","display_name":null,"funder_award_id":"XSEDE","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4469409002","display_name":null,"funder_award_id":"TG-BIO200057","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4796244077","display_name":null,"funder_award_id":"startup","funder_id":"https://openalex.org/F4320309151","funder_display_name":"Vanderbilt University"},{"id":"https://openalex.org/G5921281487","display_name":null,"funder_award_id":"number","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6332831770","display_name":null,"funder_award_id":"T32 GM008","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7908228807","display_name":null,"funder_award_id":"Molecular","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8388804679","display_name":null,"funder_award_id":"MBTP T32 GM008320","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309151","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320333026","display_name":"Department of Chemistry, Vanderbilt University","ror":null},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4313454189.pdf"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1896364650","https://openalex.org/W1992899488","https://openalex.org/W1994780695","https://openalex.org/W2004822259","https://openalex.org/W2011934361","https://openalex.org/W2037535298","https://openalex.org/W2040809566","https://openalex.org/W2043701535","https://openalex.org/W2060079863","https://openalex.org/W2064935894","https://openalex.org/W2072683434","https://openalex.org/W2094076733","https://openalex.org/W2099598754","https://openalex.org/W2100833559","https://openalex.org/W2107088292","https://openalex.org/W2126682859","https://openalex.org/W2148022166","https://openalex.org/W2170736994","https://openalex.org/W2286914510","https://openalex.org/W2294529353","https://openalex.org/W2313116527","https://openalex.org/W2320251714","https://openalex.org/W2327370752","https://openalex.org/W2404280981","https://openalex.org/W2516895464","https://openalex.org/W2593189583","https://openalex.org/W2626794769","https://openalex.org/W2735268966","https://openalex.org/W2792143480","https://openalex.org/W2892756269","https://openalex.org/W2921257516","https://openalex.org/W2923454374","https://openalex.org/W2961911698","https://openalex.org/W2990344250","https://openalex.org/W2990514783","https://openalex.org/W3087348949","https://openalex.org/W3118410948","https://openalex.org/W3183475563","https://openalex.org/W3183478041","https://openalex.org/W3193427447","https://openalex.org/W3213152276","https://openalex.org/W4221041249","https://openalex.org/W4226376464","https://openalex.org/W4284960011"],"related_works":["https://openalex.org/W4353055924","https://openalex.org/W2732388178","https://openalex.org/W2806488847","https://openalex.org/W4361279638","https://openalex.org/W2121688928","https://openalex.org/W3126783617","https://openalex.org/W3093468851","https://openalex.org/W4387012733","https://openalex.org/W2015390241","https://openalex.org/W2772651271"],"abstract_inverted_index":{"Lasso":[0],"peptides":[1,11,26],"are":[2,27,155,175],"a":[3,13,47,75,185],"subclass":[4],"of":[5,42,60,129,150,179],"ribosomally":[6],"synthesized":[7],"and":[8,22,32,40,56,69,78,87,108,195],"post-translationally":[9],"modified":[10],"with":[12,132],"slipknot":[14],"conformation.":[15],"With":[16,74],"superior":[17],"thermal":[18],"stability,":[19],"protease":[20],"resistance,":[21],"antimicrobial":[23],"activity,":[24],"lasso":[25,43,52,103,192],"promising":[28],"candidates":[29],"for":[30,50,114,191],"bioengineering":[31],"pharmaceutical":[33],"applications.":[34],"To":[35],"enable":[36],"high-throughput":[37],"computational":[38,186],"prediction":[39,194],"design":[41],"peptides,":[44],"we":[45,121,142],"developed":[46],"software,":[48],"LassoHTP,":[49],"automatic":[51],"peptide":[53,104,193],"structure":[54,86],"construction":[55],"modeling.":[57],"LassoHTP":[58,81,98,183],"consists":[59],"three":[61],"modules,":[62],"including":[63],"the":[64,85,123,151,158,172,180],"scaffold":[65],"constructor,":[66],"mutant":[67],"generator,":[68],"molecular":[70],"dynamics":[71],"(MD)":[72],"simulator.":[73],"user-provided":[76],"sequence":[77],"conformational":[79,88,112],"annotation,":[80],"can":[82],"either":[83],"generate":[84],"ensemble":[89],"as":[90],"is":[91],"or":[92,138],"conduct":[93],"random":[94],"mutagenesis.":[95],"We":[96],"used":[97],"to":[99,109,134,177,188],"construct":[100],"eight":[101],"known":[102],"structures":[105],"<i>de":[106],"novo</i>":[107],"simulate":[110],"their":[111,135],"ensembles":[113,131,153,174],"100":[115],"ns":[116],"MD":[117,152],"simulations.":[118],"For":[119],"benchmarking,":[120],"calculated":[122],"root":[124],"mean":[125],"square":[126],"deviation":[127],"(RMSD)":[128],"these":[130,145],"reference":[133],"experimental":[136],"crystal":[137],"NMR":[139],"PDB":[140,159],"structures;":[141],"also":[143,166],"compared":[144],"RMSD":[146],"values":[147],"against":[148],"those":[149,178],"that":[154,171],"initiated":[156],"from":[157],"structures.":[160],"Dihedral":[161],"principal":[162],"component":[163],"analysis":[164],"was":[165],"conducted.":[167],"The":[168],"results":[169],"show":[170],"LassoHTP-initiated":[173],"similar":[176],"PDB-initiated":[181],"ensembles.":[182],"offers":[184],"platform":[187],"develop":[189],"strategies":[190],"design.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}