{"id":"https://openalex.org/W2946614862","doi":"https://doi.org/10.1093/nar/gkz399","title":"NAPS update: network analysis of molecular dynamics data and protein\u2013nucleic acid complexes","display_name":"NAPS update: network analysis of molecular dynamics data and protein\u2013nucleic acid complexes","publication_year":2019,"publication_date":"2019-05-07","ids":{"openalex":"https://openalex.org/W2946614862","doi":"https://doi.org/10.1093/nar/gkz399","mag":"2946614862","pmid":"https://pubmed.ncbi.nlm.nih.gov/31106363"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkz399","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz399","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gkz399","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054458171","display_name":"Broto Chakrabarty","orcid":"https://orcid.org/0000-0002-4938-4426"},"institutions":[{"id":"https://openalex.org/I64189192","display_name":"International Institute of Information Technology, Hyderabad","ror":"https://ror.org/05f11g639","country_code":"IN","type":"education","lineage":["https://openalex.org/I64189192"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Broto Chakrabarty","raw_affiliation_strings":["Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology - Hyderabad 500032, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology - Hyderabad 500032, India","institution_ids":["https://openalex.org/I64189192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072398266","display_name":"Varun Naganathan","orcid":null},"institutions":[{"id":"https://openalex.org/I64189192","display_name":"International Institute of Information Technology, Hyderabad","ror":"https://ror.org/05f11g639","country_code":"IN","type":"education","lineage":["https://openalex.org/I64189192"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Varun Naganathan","raw_affiliation_strings":["Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology - Hyderabad 500032, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology - Hyderabad 500032, India","institution_ids":["https://openalex.org/I64189192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026405383","display_name":"Kanak Garg","orcid":null},"institutions":[{"id":"https://openalex.org/I64189192","display_name":"International Institute of Information Technology, Hyderabad","ror":"https://ror.org/05f11g639","country_code":"IN","type":"education","lineage":["https://openalex.org/I64189192"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Kanak Garg","raw_affiliation_strings":["Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology - Hyderabad 500032, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology - Hyderabad 500032, India","institution_ids":["https://openalex.org/I64189192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042368055","display_name":"Yash Agarwal","orcid":"https://orcid.org/0000-0001-7785-7828"},"institutions":[{"id":"https://openalex.org/I64189192","display_name":"International Institute of Information Technology, Hyderabad","ror":"https://ror.org/05f11g639","country_code":"IN","type":"education","lineage":["https://openalex.org/I64189192"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Yash Agarwal","raw_affiliation_strings":["Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology - Hyderabad 500032, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology - Hyderabad 500032, India","institution_ids":["https://openalex.org/I64189192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066775485","display_name":"Nita Parekh","orcid":"https://orcid.org/0000-0002-8737-0260"},"institutions":[{"id":"https://openalex.org/I64189192","display_name":"International Institute of Information Technology, Hyderabad","ror":"https://ror.org/05f11g639","country_code":"IN","type":"education","lineage":["https://openalex.org/I64189192"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Nita Parekh","raw_affiliation_strings":["Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology - Hyderabad 500032, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology - Hyderabad 500032, India","institution_ids":["https://openalex.org/I64189192"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5066775485"],"corresponding_institution_ids":["https://openalex.org/I64189192"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.8172,"has_fulltext":false,"cited_by_count":60,"citation_normalized_percentile":{"value":0.9161453,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"47","issue":"W1","first_page":"W462","last_page":"W470"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"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":1.0,"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/T11162","display_name":"Enzyme Structure and Function","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980999827384949,"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/nucleic-acid","display_name":"Nucleic acid","score":0.6229551434516907},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5874229073524475},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.581626832485199},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5314637422561646},{"id":"https://openalex.org/keywords/biomolecule","display_name":"Biomolecule","score":0.507136344909668},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.48499414324760437},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.43987658619880676},{"id":"https://openalex.org/keywords/protein-dynamics","display_name":"Protein dynamics","score":0.4323599338531494},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.43093040585517883},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.42655906081199646},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.4237612187862396},{"id":"https://openalex.org/keywords/allosteric-regulation","display_name":"Allosteric regulation","score":0.4174264073371887},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4008297622203827},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3841824531555176},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.17556524276733398},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.14153626561164856},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10918325185775757},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.108377605676651}],"concepts":[{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.6229551434516907},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5874229073524475},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.581626832485199},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5314637422561646},{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.507136344909668},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.48499414324760437},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.43987658619880676},{"id":"https://openalex.org/C2775981520","wikidata":"https://www.wikidata.org/wiki/Q17156992","display_name":"Protein dynamics","level":3,"score":0.4323599338531494},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.43093040585517883},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.42655906081199646},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4237612187862396},{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.4174264073371887},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4008297622203827},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3841824531555176},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.17556524276733398},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.14153626561164856},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10918325185775757},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.108377605676651},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":3,"locations":[{"id":"doi:10.1093/nar/gkz399","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz399","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:31106363","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31106363","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:5577305","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6602509","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkz399","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz399","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320717","display_name":"Department of Biotechnology, Ministry of Science and Technology, India","ror":"https://ror.org/03tjsyq23"},{"id":"https://openalex.org/F4320335273","display_name":"Oxford University Press","ror":"https://ror.org/0336mm561"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W229097380","https://openalex.org/W1525985997","https://openalex.org/W1672171675","https://openalex.org/W1674510714","https://openalex.org/W1852421212","https://openalex.org/W1863324516","https://openalex.org/W1979933191","https://openalex.org/W1980858273","https://openalex.org/W1981122373","https://openalex.org/W1982874561","https://openalex.org/W1984695931","https://openalex.org/W1987958688","https://openalex.org/W2006927892","https://openalex.org/W2008136665","https://openalex.org/W2011168681","https://openalex.org/W2012966615","https://openalex.org/W2041882488","https://openalex.org/W2042454335","https://openalex.org/W2046781968","https://openalex.org/W2047973183","https://openalex.org/W2048934130","https://openalex.org/W2049861471","https://openalex.org/W2052166746","https://openalex.org/W2057443486","https://openalex.org/W2062926294","https://openalex.org/W2067843070","https://openalex.org/W2072238363","https://openalex.org/W2076580461","https://openalex.org/W2094571158","https://openalex.org/W2101414808","https://openalex.org/W2114858005","https://openalex.org/W2141940595","https://openalex.org/W2141960720","https://openalex.org/W2142001247","https://openalex.org/W2148866967","https://openalex.org/W2159675211","https://openalex.org/W2163300188","https://openalex.org/W2163641424","https://openalex.org/W2164243919","https://openalex.org/W2166997231","https://openalex.org/W2217159534","https://openalex.org/W2345718491","https://openalex.org/W2395425574","https://openalex.org/W2404280981","https://openalex.org/W2534652523","https://openalex.org/W2554722417","https://openalex.org/W2555870966","https://openalex.org/W2611206135","https://openalex.org/W2619817401","https://openalex.org/W2783006100","https://openalex.org/W2799691204","https://openalex.org/W2803284534","https://openalex.org/W2806399642","https://openalex.org/W2894589585","https://openalex.org/W4254350734","https://openalex.org/W6608852248","https://openalex.org/W6637288986","https://openalex.org/W6679191575","https://openalex.org/W6754928003"],"related_works":["https://openalex.org/W4366407519","https://openalex.org/W2561771613","https://openalex.org/W2474016806","https://openalex.org/W2003412353","https://openalex.org/W2073871758","https://openalex.org/W2108284748","https://openalex.org/W4220959342","https://openalex.org/W2010384662","https://openalex.org/W2052504582","https://openalex.org/W2016704325"],"abstract_inverted_index":{"Network":[0],"theory":[1],"is":[2,26,169],"now":[3,68],"a":[4],"method":[5],"of":[6,66,72,76,93,102,107,113,116,119,129,137,147,178],"choice":[7],"to":[8,56,171],"gain":[9],"insights":[10],"in":[11,42,53],"understanding":[12],"protein":[13],"structure,":[14],"folding":[15],"and":[16,39,86,100,111,121,143,151,187],"function.":[17],"In":[18],"combination":[19],"with":[20,30,161],"molecular":[21],"dynamics":[22],"(MD)":[23],"simulations,":[24],"it":[25],"an":[27],"invaluable":[28],"tool":[29],"widespread":[31],"applications":[32],"such":[33],"as":[34,133,135],"analyzing":[35],"subtle":[36],"conformational":[37],"changes":[38],"flexibility":[40],"regions":[41,49],"proteins,":[43,80,148],"dynamic":[44,122],"correlation":[45],"analysis":[46,71,92,101,106,112,146],"across":[47],"distant":[48],"for":[50,61,91],"allosteric":[51],"communications,":[52],"drug":[54],"design":[55],"reveal":[57],"alternative":[58],"binding":[59],"pockets":[60],"drugs,":[62],"etc.":[63],"Updated":[64,176],"version":[65,177],"NAPS":[67,179],"facilitates":[69],"network":[70,98,115,154],"the":[73,117,130,138,173],"complete":[74],"repertoire":[75],"these":[77,108],"biomolecules,":[78],"i.e.,":[79],"protein-protein/nucleic":[81],"acid":[82,126],"complexes,":[83,127],"MD":[84,94,152],"trajectories,":[85,153],"RNA.":[87],"Various":[88],"options":[89],"provided":[90,170],"trajectories":[95,120],"include":[96],"individual":[97],"construction":[99,110,155],"intermediate":[103],"time-steps,":[104],"comparative":[105],"networks,":[109],"average":[114],"ensemble":[118],"cross-correlations.":[123],"For":[124,145],"protein-nucleic":[125],"networks":[128],"whole":[131],"complex":[132],"well":[134],"that":[136],"interface":[139],"can":[140],"be":[141],"constructed":[142],"analyzed.":[144],"protein-protein":[149],"complexes":[150],"based":[156],"on":[157],"inter-residue":[158],"interaction":[159],"energies":[160],"realistic":[162],"edge-weights":[163],"obtained":[164],"from":[165],"standard":[166],"force":[167],"fields":[168],"capture":[172],"atomistic":[174],"details.":[175],"also":[180],"provides":[181],"improved":[182],"visualization":[183],"features,":[184],"interactive":[185],"plots":[186],"bulk":[188],"execution.":[189],"URL:":[190],"http://bioinf.iiit.ac.in/NAPS/.":[191]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
