{"id":"https://openalex.org/W4403670275","doi":"https://doi.org/10.1007/s10822-024-00575-z","title":"Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model","display_name":"Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model","publication_year":2024,"publication_date":"2024-10-24","ids":{"openalex":"https://openalex.org/W4403670275","doi":"https://doi.org/10.1007/s10822-024-00575-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/39443337"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-024-00575-z","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-024-00575-z","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059197605","display_name":"Phuc-Chau Do","orcid":"https://orcid.org/0000-0002-0280-0816"},"institutions":[{"id":"https://openalex.org/I123565023","display_name":"Vietnam National University Ho Chi Minh City","ror":"https://ror.org/00waaqh38","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023"]},{"id":"https://openalex.org/I228151691","display_name":"Ho Chi Minh City International University","ror":"https://ror.org/003szmg30","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I228151691"]}],"countries":["VN"],"is_corresponding":true,"raw_author_name":"Phuc-Chau Do","raw_affiliation_strings":["School of Biotechnology, International University, Hochiminh City, 700000, Vietnam. dnpchau@hcmiu.edu.vn","Vietnam National University - HCMC, Hochiminh City, 700000, Vietnam. dnpchau@hcmiu.edu.vn"],"affiliations":[{"raw_affiliation_string":"School of Biotechnology, International University, Hochiminh City, 700000, Vietnam. dnpchau@hcmiu.edu.vn","institution_ids":["https://openalex.org/I228151691"]},{"raw_affiliation_string":"Vietnam National University - HCMC, Hochiminh City, 700000, Vietnam. dnpchau@hcmiu.edu.vn","institution_ids":["https://openalex.org/I123565023"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001968267","display_name":"Vy Truc Le","orcid":"https://orcid.org/0009-0002-1008-2380"},"institutions":[{"id":"https://openalex.org/I123565023","display_name":"Vietnam National University Ho Chi Minh City","ror":"https://ror.org/00waaqh38","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023"]},{"id":"https://openalex.org/I228151691","display_name":"Ho Chi Minh City International University","ror":"https://ror.org/003szmg30","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I228151691"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Vy T. T. Le","raw_affiliation_strings":["School of Biotechnology, International University, Hochiminh City, 700000, Vietnam","Vietnam National University - HCMC, Hochiminh City, 700000, Vietnam"],"affiliations":[{"raw_affiliation_string":"School of Biotechnology, International University, Hochiminh City, 700000, Vietnam","institution_ids":["https://openalex.org/I228151691"]},{"raw_affiliation_string":"Vietnam National University - HCMC, Hochiminh City, 700000, Vietnam","institution_ids":["https://openalex.org/I123565023"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5059197605"],"corresponding_institution_ids":["https://openalex.org/I123565023","https://openalex.org/I228151691"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":0.8061,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.75085559,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"38","issue":"1","first_page":"34","last_page":"34"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11124","display_name":"Protein purification and stability","score":0.9991999864578247,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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/antibody","display_name":"Antibody","score":0.7317091226577759},{"id":"https://openalex.org/keywords/monoclonal-antibody","display_name":"Monoclonal antibody","score":0.665076494216919},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.5529239773750305},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5528294444084167},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5321763157844543},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.5108880400657654},{"id":"https://openalex.org/keywords/immunoglobulin-light-chain","display_name":"Immunoglobulin light chain","score":0.47328847646713257},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4617500603199005},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4001087248325348},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.3416820168495178},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.32448285818099976},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2725035548210144},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.24429470300674438},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.21738797426223755},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.19889238476753235}],"concepts":[{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.7317091226577759},{"id":"https://openalex.org/C542903549","wikidata":"https://www.wikidata.org/wiki/Q422248","display_name":"Monoclonal antibody","level":3,"score":0.665076494216919},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.5529239773750305},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5528294444084167},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5321763157844543},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5108880400657654},{"id":"https://openalex.org/C36394416","wikidata":"https://www.wikidata.org/wiki/Q949267","display_name":"Immunoglobulin light chain","level":3,"score":0.47328847646713257},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4617500603199005},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4001087248325348},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.3416820168495178},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.32448285818099976},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2725035548210144},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.24429470300674438},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.21738797426223755},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.19889238476753235},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000911","descriptor_name":"Antibodies, Monoclonal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007140","descriptor_name":"Immunoglobulin Fab Fragments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007140","descriptor_name":"Immunoglobulin Fab Fragments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007140","descriptor_name":"Immunoglobulin Fab Fragments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007140","descriptor_name":"Immunoglobulin Fab Fragments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007140","descriptor_name":"Immunoglobulin Fab Fragments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000276","qualifier_name":"immunology","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":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","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},{"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":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D057134","descriptor_name":"Antibodies, Neutralizing","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-024-00575-z","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-024-00575-z","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:39443337","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39443337","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3852400320","display_name":null,"funder_award_id":"VINIF.2020.TS","funder_id":"https://openalex.org/F4320328994","funder_display_name":"Qu\u1ef9 \u0110\u1ed5i m\u1edbi s\u00e1ng t\u1ea1o Vingroup"}],"funders":[{"id":"https://openalex.org/F4320328994","display_name":"Qu\u1ef9 \u0110\u1ed5i m\u1edbi s\u00e1ng t\u1ea1o Vingroup","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":68,"referenced_works":["https://openalex.org/W95014119","https://openalex.org/W203363010","https://openalex.org/W1855086894","https://openalex.org/W1968285218","https://openalex.org/W1971021060","https://openalex.org/W1981737096","https://openalex.org/W1997475883","https://openalex.org/W2003811296","https://openalex.org/W2005594958","https://openalex.org/W2014109976","https://openalex.org/W2014699651","https://openalex.org/W2019394341","https://openalex.org/W2043812489","https://openalex.org/W2053538195","https://openalex.org/W2074951455","https://openalex.org/W2094225605","https://openalex.org/W2100833559","https://openalex.org/W2101165138","https://openalex.org/W2129138941","https://openalex.org/W2131262274","https://openalex.org/W2132629607","https://openalex.org/W2135732933","https://openalex.org/W2143467722","https://openalex.org/W2146982119","https://openalex.org/W2154019529","https://openalex.org/W2157116486","https://openalex.org/W2157411488","https://openalex.org/W2158529560","https://openalex.org/W2160544821","https://openalex.org/W2162922414","https://openalex.org/W2246074199","https://openalex.org/W2270909071","https://openalex.org/W2344483747","https://openalex.org/W2549938765","https://openalex.org/W2613779271","https://openalex.org/W2786695043","https://openalex.org/W2797103865","https://openalex.org/W2835938797","https://openalex.org/W2884406458","https://openalex.org/W2898078665","https://openalex.org/W2899363469","https://openalex.org/W2913847447","https://openalex.org/W2965936806","https://openalex.org/W2966972453","https://openalex.org/W2969351103","https://openalex.org/W2990427812","https://openalex.org/W2993866869","https://openalex.org/W2995491930","https://openalex.org/W3081286612","https://openalex.org/W3087085381","https://openalex.org/W3100210861","https://openalex.org/W3113773638","https://openalex.org/W3130921941","https://openalex.org/W3136815103","https://openalex.org/W3156442133","https://openalex.org/W3184560074","https://openalex.org/W3185197558","https://openalex.org/W3213441803","https://openalex.org/W4230654908","https://openalex.org/W4235384839","https://openalex.org/W4242289937","https://openalex.org/W4284970640","https://openalex.org/W4292738499","https://openalex.org/W4309022734","https://openalex.org/W4309363873","https://openalex.org/W4321614983","https://openalex.org/W4327950159","https://openalex.org/W6826364103"],"related_works":["https://openalex.org/W2178864683","https://openalex.org/W2901678674","https://openalex.org/W2057057912","https://openalex.org/W1997837553","https://openalex.org/W3006749446","https://openalex.org/W2043042073","https://openalex.org/W2006486421","https://openalex.org/W4243269481","https://openalex.org/W4399786742","https://openalex.org/W2392140958"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-01T17:29:45.350535","created_date":"2025-10-10T00:00:00"}
