{"id":"https://openalex.org/W2515260495","doi":"https://doi.org/10.4137/bbi.s40427","title":"Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives \u2013 An in Silico Approach","display_name":"Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives \u2013 An in Silico Approach","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2515260495","doi":"https://doi.org/10.4137/bbi.s40427","mag":"2515260495","pmid":"https://pubmed.ncbi.nlm.nih.gov/27594785","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5004996"},"language":"en","primary_location":{"id":"doi:10.4137/bbi.s40427","doi":"https://doi.org/10.4137/bbi.s40427","is_oa":true,"landing_page_url":"https://doi.org/10.4137/bbi.s40427","pdf_url":"https://journals.sagepub.com/doi/pdf/10.4137/BBI.S40427","source":{"id":"https://openalex.org/S113186628","display_name":"Bioinformatics and Biology Insights","issn_l":"1177-9322","issn":["1177-9322"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","jufo-1","ki-jl-1","norway-1","oarl","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics and Biology Insights","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.sagepub.com/doi/pdf/10.4137/BBI.S40427","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027553529","display_name":"Subhomoi Borkotoky","orcid":"https://orcid.org/0000-0001-6752-4296","observed_orcids":["https://orcid.org/0000-0001-6752-4296"]},"institutions":[{"id":"https://openalex.org/I175691731","display_name":"Pondicherry University","ror":"https://ror.org/01a3mef16","country_code":"IN","type":"education","lineage":["https://openalex.org/I175691731"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Subhomoi Borkotoky","raw_affiliation_strings":["Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India","institution_ids":["https://openalex.org/I175691731"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044154029","display_name":"Chetan Kumar Meena","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I175691731","display_name":"Pondicherry University","ror":"https://ror.org/01a3mef16","country_code":"IN","type":"education","lineage":["https://openalex.org/I175691731"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Chetan Kumar Meena","raw_affiliation_strings":["Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India","institution_ids":["https://openalex.org/I175691731"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072405725","display_name":"Ayaluru Murali","orcid":"https://orcid.org/0000-0001-6406-6840","observed_orcids":["https://orcid.org/0000-0001-6406-6840"]},"institutions":[{"id":"https://openalex.org/I175691731","display_name":"Pondicherry University","ror":"https://ror.org/01a3mef16","country_code":"IN","type":"education","lineage":["https://openalex.org/I175691731"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Ayaluru Murali","raw_affiliation_strings":["Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India","institution_ids":["https://openalex.org/I175691731"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5072405725"],"corresponding_institution_ids":["https://openalex.org/I175691731"],"apc_list":{"value":2650,"currency":"USD","value_usd":2650},"apc_paid":{"value":2650,"currency":"USD","value_usd":2650},"fwci":2.4531,"has_fulltext":false,"cited_by_count":45,"citation_normalized_percentile":{"value":0.89231591,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"10","issue":null,"first_page":"BBI.S40427","last_page":"BBI.S40427"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9570000171661377,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9570000171661377,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.030700000002980232,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.001500000013038516,"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/t7-rna-polymerase","display_name":"T7 RNA polymerase","score":1.0},{"id":"https://openalex.org/keywords/heparin","display_name":"heparin","score":0.9919999837875366},{"id":"https://openalex.org/keywords/low-molecular-weight-heparin","display_name":"low molecular weight heparin","score":0.9700000286102295},{"id":"https://openalex.org/keywords/enoxaparin","display_name":"enoxaparin","score":0.9919999837875366},{"id":"https://openalex.org/keywords/rna-polymerase-inhibition","display_name":"RNA polymerase inhibition","score":0.7289999723434448},{"id":"https://openalex.org/keywords/protein-ligand-binding","display_name":"protein-ligand binding","score":0.8180000185966492},{"id":"https://openalex.org/keywords/binding-free-energy","display_name":"binding free energy","score":0.8159999847412109},{"id":"https://openalex.org/keywords/molecular-docking","display_name":"molecular docking","score":0.7590000033378601},{"id":"https://openalex.org/keywords/molecular-dynamics-simulation","display_name":"molecular dynamics simulation","score":0.8130000233650208}],"concepts":[{"id":"https://openalex.org/C25057246","wikidata":"https://www.wikidata.org/wiki/Q1344441","display_name":"Molecular mechanics","level":3,"score":0.6280205249786377},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6138231158256531},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5778045654296875},{"id":"https://openalex.org/C82381507","wikidata":"https://www.wikidata.org/wiki/Q416878","display_name":"Polymerase","level":3,"score":0.573352038860321},{"id":"https://openalex.org/C2777557582","wikidata":"https://www.wikidata.org/wiki/Q190016","display_name":"Heparin","level":2,"score":0.551651120185852},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5225409865379333},{"id":"https://openalex.org/C2776449523","wikidata":"https://www.wikidata.org/wiki/Q272631","display_name":"RNA polymerase","level":4,"score":0.510751485824585},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.48161619901657104},{"id":"https://openalex.org/C126061179","wikidata":"https://www.wikidata.org/wiki/Q189627","display_name":"van der Waals force","level":3,"score":0.4773707091808319},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.444587379693985},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.41488081216812134},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4117969870567322},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4111633002758026},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.34262827038764954},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.34206610918045044},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.32075047492980957},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2535296678543091},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.18254756927490234},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.14157333970069885},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13573792576789856},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0863756537437439},{"id":"https://openalex.org/C2780471494","wikidata":"https://www.wikidata.org/wiki/Q146505","display_name":"Solvent","level":2,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.4137/bbi.s40427","doi":"https://doi.org/10.4137/bbi.s40427","is_oa":true,"landing_page_url":"https://doi.org/10.4137/bbi.s40427","pdf_url":"https://journals.sagepub.com/doi/pdf/10.4137/BBI.S40427","source":{"id":"https://openalex.org/S113186628","display_name":"Bioinformatics and Biology Insights","issn_l":"1177-9322","issn":["1177-9322"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","jufo-1","ki-jl-1","norway-1","oarl","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics and Biology Insights","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5004996","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5004996","pdf_url":null,"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,"listed_in":[],"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":"Bioinform Biol Insights","raw_type":"Text"},{"id":"pmid:27594785","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27594785","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,"listed_in":[],"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 and biology insights","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:258e076f2ba645aaac4a6ed4f171d9b0","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/258e076f2ba645aaac4a6ed4f171d9b0","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics and Biology Insights, Vol 10 (2016)","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:bd3164f5db5e4f8e9f589f5220430130","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/bd3164f5db5e4f8e9f589f5220430130","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics and Biology Insights, Vol 2016, Iss 10, Pp 155-166 (2016)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.4137/bbi.s40427","doi":"https://doi.org/10.4137/bbi.s40427","is_oa":true,"landing_page_url":"https://doi.org/10.4137/bbi.s40427","pdf_url":"https://journals.sagepub.com/doi/pdf/10.4137/BBI.S40427","source":{"id":"https://openalex.org/S113186628","display_name":"Bioinformatics and Biology Insights","issn_l":"1177-9322","issn":["1177-9322"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","jufo-1","ki-jl-1","norway-1","oarl","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics and Biology Insights","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2515260495.pdf"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1493628530","https://openalex.org/W1566389069","https://openalex.org/W1591867940","https://openalex.org/W1607931568","https://openalex.org/W1965642201","https://openalex.org/W1966319705","https://openalex.org/W1971361446","https://openalex.org/W1974148133","https://openalex.org/W1975679166","https://openalex.org/W1975993749","https://openalex.org/W1977937840","https://openalex.org/W1977949865","https://openalex.org/W1990059495","https://openalex.org/W1992091655","https://openalex.org/W2008908797","https://openalex.org/W2012700578","https://openalex.org/W2029582401","https://openalex.org/W2031106427","https://openalex.org/W2032817710","https://openalex.org/W2037312364","https://openalex.org/W2040066175","https://openalex.org/W2044172327","https://openalex.org/W2045787584","https://openalex.org/W2045811760","https://openalex.org/W2057477511","https://openalex.org/W2057520657","https://openalex.org/W2058769888","https://openalex.org/W2067489441","https://openalex.org/W2071737815","https://openalex.org/W2074473216","https://openalex.org/W2085577715","https://openalex.org/W2095111544","https://openalex.org/W2096071764","https://openalex.org/W2100251789","https://openalex.org/W2102377211","https://openalex.org/W2102686303","https://openalex.org/W2108994910","https://openalex.org/W2113814538","https://openalex.org/W2114167986","https://openalex.org/W2114367386","https://openalex.org/W2127522551","https://openalex.org/W2127553917","https://openalex.org/W2128572087","https://openalex.org/W2132629607","https://openalex.org/W2145699026","https://openalex.org/W2147282719","https://openalex.org/W2153344241","https://openalex.org/W2154646453","https://openalex.org/W2157281740","https://openalex.org/W2161062388","https://openalex.org/W2170540925","https://openalex.org/W2171268876","https://openalex.org/W2174397546","https://openalex.org/W2198661776","https://openalex.org/W2333610724","https://openalex.org/W4211054902"],"related_works":["https://openalex.org/W1549680332","https://openalex.org/W2151369884","https://openalex.org/W1554071050","https://openalex.org/W2012668816","https://openalex.org/W2757527077","https://openalex.org/W2416617184","https://openalex.org/W2343374373","https://openalex.org/W2130520875","https://openalex.org/W2395067321","https://openalex.org/W2167934763"],"abstract_inverted_index":{"The":[0,79,215],"single":[1],"subunit":[2],"T7":[3],"RNA":[4,33],"polymerase":[5],"(T7RNAP)":[6],"is":[7,24,42],"a":[8,25],"model":[9],"enzyme":[10],"for":[11,17,143,176,208,224],"studying":[12],"the":[13,52,82,88,101,109,117,139,144,155,188,225],"transcription":[14],"process":[15],"and":[16,20,31,40,60,91,104,134,171,201,231,236],"various":[18],"biochemical":[19],"biophysical":[21],"studies.":[22],"Heparin":[23],"commonly":[26],"used":[27],"inhibitor":[28],"against":[29,234],"T7RNAP":[30,41,76,235],"other":[32],"polymerases.":[34],"However,":[35],"exact":[36],"interaction":[37],"between":[38],"heparin":[39,56,59,177],"still":[43],"not":[44],"completely":[45],"understood.":[46],"In":[47],"this":[48,219],"work,":[49],"we":[50],"analyzed":[51],"binding":[53,105,145,209],"pattern":[54],"of":[55,62,75,81,100,108,210,229],"by":[57,86],"docking":[58,87],"few":[61],"its":[63],"low":[64,120],"molecular":[65,93,121],"weight":[66,122],"derivatives":[67],"to":[68,115],"T7RNAP,":[69],"which":[70,204],"helps":[71],"in":[72,186],"better":[73],"understanding":[74],"inhibition":[77],"mechanism.":[78],"efficiency":[80],"compounds":[83,90],"was":[84],"calculated":[85],"selected":[89],"post-docking":[92],"mechanics/generalized":[94],"Born":[95],"surface":[96],"area":[97],"analysis.":[98],"Evaluation":[99],"simulation":[102,112],"trajectories":[103],"free":[106,125,149],"energies":[107],"complexes":[110,190],"after":[111],"showed":[113],"enoxaparin":[114],"be":[116,206,222],"best":[118],"among":[119],"heparins.":[123],"Binding":[124],"energy":[126,137,150],"analysis":[127,152],"revealed":[128,153],"that":[129,154],"van":[130],"der":[131],"Waals":[132],"interactions":[133],"polar":[135],"solvation":[136],"provided":[138],"substantial":[140],"driving":[141],"force":[142],"process.":[146],"Furthermore,":[147],"per-residue":[148],"decomposition":[151],"residues":[156],"Asp":[157,159,161,167,172,193,202],"471,":[158],"506,":[160,194],"537,":[162],"Tyr":[163,195],"571,":[164,196],"Met":[165,197],"635,":[166,198],"653,":[168,203],"Pro":[169],"780,":[170],"812":[173],"are":[174],"important":[175],"interaction.":[178],"Apart":[179],"from":[180,192,218],"these":[181],"residues,":[182],"most":[183],"favorable":[184],"contribution":[185],"all":[187],"three":[189],"came":[191],"Glu":[199],"652,":[200],"can":[205],"essential":[207],"heparin-like":[211],"structures":[212],"with":[213],"T7RNAP.":[214],"results":[216],"obtained":[217],"study":[220],"will":[221],"valuable":[223],"future":[226],"rational":[227],"design":[228],"novel":[230],"potent":[232],"inhibitors":[233],"related":[237],"proteins.":[238]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2}],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2016-09-16T00:00:00"}
