{"id":"https://openalex.org/W4399608146","doi":"https://doi.org/10.1093/bioinformatics/btae313","title":"MolDy: molecular dynamics simulation made easy","display_name":"MolDy: molecular dynamics simulation made easy","publication_year":2024,"publication_date":"2024-06-01","ids":{"openalex":"https://openalex.org/W4399608146","doi":"https://doi.org/10.1093/bioinformatics/btae313","pmid":"https://pubmed.ncbi.nlm.nih.gov/38867698"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae313","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae313","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/6/btae313/58283350/btae313.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/40/6/btae313/58283350/btae313.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001325857","display_name":"Mohd Imran Khan","orcid":"https://orcid.org/0009-0002-8896-9619"},"institutions":[{"id":"https://openalex.org/I2800965796","display_name":"King Faisal Specialist Hospital & Research Centre","ror":"https://ror.org/05n0wgt02","country_code":"SA","type":"healthcare","lineage":["https://openalex.org/I2800965796"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Mohd Imran Khan","raw_affiliation_strings":["Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","Research Center, King Faisal Specialist Hospital and Research Center , Jeddah 21589, Saudi Arabia"],"raw_orcid":"https://orcid.org/0009-0002-8896-9619","affiliations":[{"raw_affiliation_string":"Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","institution_ids":[]},{"raw_affiliation_string":"Research Center, King Faisal Specialist Hospital and Research Center , Jeddah 21589, Saudi Arabia","institution_ids":["https://openalex.org/I2800965796"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113249957","display_name":"Sheetal Pathania","orcid":null},"institutions":[{"id":"https://openalex.org/I2800965796","display_name":"King Faisal Specialist Hospital & Research Centre","ror":"https://ror.org/05n0wgt02","country_code":"SA","type":"healthcare","lineage":["https://openalex.org/I2800965796"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Mohd Imran Khan","raw_affiliation_strings":["Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","Research Center, King Faisal Specialist Hospital and Research Center , Jeddah 21589, Saudi Arabia"],"raw_orcid":"https://orcid.org/0009-0002-8896-9619","affiliations":[{"raw_affiliation_string":"Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","institution_ids":[]},{"raw_affiliation_string":"Research Center, King Faisal Specialist Hospital and Research Center , Jeddah 21589, Saudi Arabia","institution_ids":["https://openalex.org/I2800965796"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077795722","display_name":"Mohammed W. Al-Rabia","orcid":"https://orcid.org/0000-0002-1578-1810"},"institutions":[{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Sheetal Pathania","raw_affiliation_strings":["Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdul Aziz University , Jeddah 21589, Saudi Arabia","Department of Clinical and Molecular Microbiology Laboratory, King Abdulaziz University Hospital , Jeddah 21589, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","institution_ids":[]},{"raw_affiliation_string":"Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdul Aziz University , Jeddah 21589, Saudi Arabia","institution_ids":[]},{"raw_affiliation_string":"Department of Clinical and Molecular Microbiology Laboratory, King Abdulaziz University Hospital , Jeddah 21589, Saudi Arabia","institution_ids":["https://openalex.org/I185163786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066029953","display_name":"A.S. Ethayathulla","orcid":"https://orcid.org/0000-0001-8958-3916"},"institutions":[{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]},{"id":"https://openalex.org/I63739035","display_name":"All India Institute of Medical Sciences","ror":"https://ror.org/02dwcqs71","country_code":"IN","type":"education","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210148677","https://openalex.org/I63739035"]}],"countries":["IN","SA"],"is_corresponding":false,"raw_author_name":"Mohammed W Al-Rabia","raw_affiliation_strings":["Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdul Aziz University , Jeddah 21589, Saudi Arabia","Department of Clinical and Molecular Microbiology Laboratory, King Abdulaziz University Hospital , Jeddah 21589, Saudi Arabia","Department of Biophysics, All India Institute of Medical Sciences , New Delhi 110029, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdul Aziz University , Jeddah 21589, Saudi Arabia","institution_ids":[]},{"raw_affiliation_string":"Department of Clinical and Molecular Microbiology Laboratory, King Abdulaziz University Hospital , Jeddah 21589, Saudi Arabia","institution_ids":["https://openalex.org/I185163786"]},{"raw_affiliation_string":"Department of Biophysics, All India Institute of Medical Sciences , New Delhi 110029, India","institution_ids":["https://openalex.org/I63739035"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046592525","display_name":"Mohammad Imran Khan","orcid":"https://orcid.org/0000-0001-5832-5017"},"institutions":[{"id":"https://openalex.org/I2800965796","display_name":"King Faisal Specialist Hospital & Research Centre","ror":"https://ror.org/05n0wgt02","country_code":"SA","type":"healthcare","lineage":["https://openalex.org/I2800965796"]},{"id":"https://openalex.org/I63739035","display_name":"All India Institute of Medical Sciences","ror":"https://ror.org/02dwcqs71","country_code":"IN","type":"education","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210148677","https://openalex.org/I63739035"]}],"countries":["IN","SA"],"is_corresponding":false,"raw_author_name":"Abdul S Ethayathulla","raw_affiliation_strings":["Department of Biophysics, All India Institute of Medical Sciences , New Delhi 110029, India","Research Center, King Faisal Specialist Hospital and Research Center , Jeddah 21589, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biophysics, All India Institute of Medical Sciences , New Delhi 110029, India","institution_ids":["https://openalex.org/I63739035"]},{"raw_affiliation_string":"Research Center, King Faisal Specialist Hospital and Research Center , Jeddah 21589, Saudi Arabia","institution_ids":["https://openalex.org/I2800965796"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019957221","display_name":"Khaled S. Allemailem","orcid":"https://orcid.org/0000-0002-6486-9835"},"institutions":[{"id":"https://openalex.org/I156216236","display_name":"Qassim University","ror":"https://ror.org/01wsfe280","country_code":"SA","type":"education","lineage":["https://openalex.org/I156216236"]},{"id":"https://openalex.org/I2800965796","display_name":"King Faisal Specialist Hospital & Research Centre","ror":"https://ror.org/05n0wgt02","country_code":"SA","type":"healthcare","lineage":["https://openalex.org/I2800965796"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Mohammad Imran Khan","raw_affiliation_strings":["Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","Research Center, King Faisal Specialist Hospital and Research Center , Jeddah 21589, Saudi Arabia","Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Buraydah 51452, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","institution_ids":[]},{"raw_affiliation_string":"Research Center, King Faisal Specialist Hospital and Research Center , Jeddah 21589, Saudi Arabia","institution_ids":["https://openalex.org/I2800965796"]},{"raw_affiliation_string":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Buraydah 51452, Saudi Arabia","institution_ids":["https://openalex.org/I156216236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057276680","display_name":"Mohd Azam","orcid":"https://orcid.org/0000-0002-4623-9557"},"institutions":[{"id":"https://openalex.org/I156216236","display_name":"Qassim University","ror":"https://ror.org/01wsfe280","country_code":"SA","type":"education","lineage":["https://openalex.org/I156216236"]},{"id":"https://openalex.org/I2800965796","display_name":"King Faisal Specialist Hospital & Research Centre","ror":"https://ror.org/05n0wgt02","country_code":"SA","type":"healthcare","lineage":["https://openalex.org/I2800965796"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Mohammad Imran Khan","raw_affiliation_strings":["Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","Research Center, King Faisal Specialist Hospital and Research Center , Jeddah 21589, Saudi Arabia","Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Buraydah 51452, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","institution_ids":[]},{"raw_affiliation_string":"Research Center, King Faisal Specialist Hospital and Research Center , Jeddah 21589, Saudi Arabia","institution_ids":["https://openalex.org/I2800965796"]},{"raw_affiliation_string":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Buraydah 51452, Saudi Arabia","institution_ids":["https://openalex.org/I156216236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012588705","display_name":"Gururao Hariprasad","orcid":"https://orcid.org/0000-0003-1179-2464"},"institutions":[{"id":"https://openalex.org/I156216236","display_name":"Qassim University","ror":"https://ror.org/01wsfe280","country_code":"SA","type":"education","lineage":["https://openalex.org/I156216236"]},{"id":"https://openalex.org/I63739035","display_name":"All India Institute of Medical Sciences","ror":"https://ror.org/02dwcqs71","country_code":"IN","type":"education","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210148677","https://openalex.org/I63739035"]}],"countries":["IN","SA"],"is_corresponding":false,"raw_author_name":"Khaled S Allemailem","raw_affiliation_strings":["Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Buraydah 51452, Saudi Arabia","Department of Biophysics, All India Institute of Medical Sciences , New Delhi 110029, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Buraydah 51452, Saudi Arabia","institution_ids":["https://openalex.org/I156216236"]},{"raw_affiliation_string":"Department of Biophysics, All India Institute of Medical Sciences , New Delhi 110029, India","institution_ids":["https://openalex.org/I63739035"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011709552","display_name":"Mohammad Imran","orcid":null},"institutions":[{"id":"https://openalex.org/I156216236","display_name":"Qassim University","ror":"https://ror.org/01wsfe280","country_code":"SA","type":"education","lineage":["https://openalex.org/I156216236"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Mohd Azam","raw_affiliation_strings":["Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Buraydah 51452, Saudi Arabia","Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India"],"raw_orcid":"https://orcid.org/0000-0002-4623-9557","affiliations":[{"raw_affiliation_string":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Buraydah 51452, Saudi Arabia","institution_ids":["https://openalex.org/I156216236"]},{"raw_affiliation_string":"Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012588705","display_name":"Gururao Hariprasad","orcid":"https://orcid.org/0000-0003-1179-2464"},"institutions":[{"id":"https://openalex.org/I63739035","display_name":"All India Institute of Medical Sciences","ror":"https://ror.org/02dwcqs71","country_code":"IN","type":"education","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210148677","https://openalex.org/I63739035"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Gururao Hariprasad","raw_affiliation_strings":["Department of Biophysics, All India Institute of Medical Sciences , New Delhi 110029, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biophysics, All India Institute of Medical Sciences , New Delhi 110029, India","institution_ids":["https://openalex.org/I63739035"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011709552","display_name":"Mohammad Imran","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Mohammad Azhar Imran","raw_affiliation_strings":["Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics, AIBR Artificial Intelligence and Biochemical Research Pvt. Ltd. , New Delhi 110076, India","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5001325857","https://openalex.org/A5011709552","https://openalex.org/A5012588705","https://openalex.org/A5057276680"],"corresponding_institution_ids":["https://openalex.org/I156216236","https://openalex.org/I2800965796","https://openalex.org/I63739035"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1172,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.76454232,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"40","issue":"6","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":0.5803999900817871,"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":0.5803999900817871,"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":0.11840000003576279,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.05400000140070915,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8213878870010376},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8180043697357178},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.7493079900741577},{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.6949277520179749},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5646557807922363},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5596010088920593},{"id":"https://openalex.org/keywords/bridging","display_name":"Bridging (networking)","score":0.546619713306427},{"id":"https://openalex.org/keywords/macro","display_name":"Macro","score":0.5431680679321289},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4935654401779175},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.48236411809921265},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.43082284927368164},{"id":"https://openalex.org/keywords/compiler","display_name":"Compiler","score":0.4272821247577667},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3411058783531189},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.324022114276886},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.32191139459609985}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8213878870010376},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8180043697357178},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7493079900741577},{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.6949277520179749},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5646557807922363},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5596010088920593},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.546619713306427},{"id":"https://openalex.org/C166955791","wikidata":"https://www.wikidata.org/wiki/Q629579","display_name":"Macro","level":2,"score":0.5431680679321289},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4935654401779175},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.48236411809921265},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.43082284927368164},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.4272821247577667},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3411058783531189},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.324022114276886},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.32191139459609985},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae313","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae313","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/6/btae313/58283350/btae313.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38867698","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38867698","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11187490","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11187490","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11187490/pdf/btae313.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae313","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae313","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/6/btae313/58283350/btae313.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322322","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4399608146.pdf"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W2039042916","https://openalex.org/W2133620840","https://openalex.org/W2160544821","https://openalex.org/W2581729559","https://openalex.org/W2884323962","https://openalex.org/W2948831670","https://openalex.org/W2972485984","https://openalex.org/W3036997165","https://openalex.org/W4229447405","https://openalex.org/W4282918903","https://openalex.org/W4285387825","https://openalex.org/W4391383720"],"related_works":["https://openalex.org/W2331989206","https://openalex.org/W3173828731","https://openalex.org/W45658120","https://openalex.org/W2008612003","https://openalex.org/W613088223","https://openalex.org/W4287121746","https://openalex.org/W2045950409","https://openalex.org/W4394260427","https://openalex.org/W2739025131","https://openalex.org/W4205178530"],"abstract_inverted_index":{"MOTIVATION:":[0],"Molecular":[1],"dynamics":[2],"(MD)":[3],"is":[4,9,33,50,194],"a":[5,53,93,152],"computational":[6],"experiment":[7],"that":[8],"crucial":[10],"for":[11,60,87,158,176,185,187,205],"understanding":[12],"the":[13,24,34,64,99,106,118,140,180],"structure":[14],"of":[15,29,126,132,146,167],"biological":[16],"macro":[17],"and":[18,23,39,55,68,101,109,116,123,178,207,212],"micro":[19],"molecules,":[20],"their":[21],"folding,":[22],"inter-molecular":[25],"interactions.":[26],"Accurate":[27],"knowledge":[28,145],"these":[30],"structural":[31],"features":[32],"cornerstone":[35],"in":[36],"drug":[37],"development":[38],"elucidating":[40],"macromolecules":[41],"functions.":[42],"The":[43,112,130],"open-source":[44],"GROMACS":[45],"biomolecular":[46],"MD":[47,74,83],"simulation":[48,58,84,121],"program":[49,59],"recognized":[51],"as":[52,197],"reliable":[54],"frequently":[56],"used":[57],"its":[61],"precision.":[62],"However,":[63],"user":[65,95,119,203],"requires":[66],"expertise,":[67],"scripting":[69],"skills":[70],"to":[71,142],"carrying":[72],"out":[73],"simulations.":[75],"RESULTS:":[76],"We":[77],"have":[78,143],"developed":[79],"an":[80],"end-to-end":[81],"interactive":[82],"application,":[85],"MolDy":[86,133,193],"Gromacs.":[88],"This":[89],"front-end":[90],"application":[91],"provides":[92,117,183],"customizable":[94],"interface":[96],"integrated":[97],"with":[98,120,164,202],"Python":[100],"Perl-based":[102],"logical":[103],"backend":[104],"connecting":[105],"Linux":[107],"shell":[108],"Gromacs":[110],"software.":[111],"tool":[113],"performs":[114],"analysis":[115],"trajectories":[122],"graphical":[124],"representations":[125],"relevant":[127],"biophysical":[128],"parameters.":[129],"advantages":[131],"are":[134],"(i)":[135],"user-friendly,":[136],"does":[137],"not":[138],"requiring":[139],"researcher":[141],"prior":[144],"Linux;":[147],"(ii)":[148],"easy":[149],"installation":[150,206],"by":[151],"single":[153],"command;":[154],"(iii)":[155],"freely":[156,196],"available":[157,195],"academic":[159],"research;":[160],"(iv)":[161],"can":[162],"run":[163],"minimum":[165],"configuration":[166],"operating":[168],"systems;":[169],"(v)":[170],"has":[171],"valid":[172],"default":[173],"prefilled":[174],"parameters":[175],"beginners,":[177],"at":[179],"same":[181],"time":[182],"scope":[184],"modifications":[186],"expert":[188],"users.":[189],"AVAILABILITY":[190],"AND":[191],"IMPLEMENTATION:":[192],"compressed":[198],"source":[199],"code":[200],"files":[201],"manual":[204],"operation":[208],"on":[209,213],"GitHub:":[210],"https://github.com/AIBResearchMolDy/Moldyv01.git":[211],"https://aibresearch.com/innovations.":[214]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-13T05:41:17.278356","created_date":"2025-10-10T00:00:00"}
