{"id":"https://openalex.org/W2003191300","doi":"https://doi.org/10.1007/s00894-014-2283-8","title":"REMD and umbrella sampling simulations to probe the energy barrier of the folding pathways of engrailed homeodomain","display_name":"REMD and umbrella sampling simulations to probe the energy barrier of the folding pathways of engrailed homeodomain","publication_year":2014,"publication_date":"2014-05-26","ids":{"openalex":"https://openalex.org/W2003191300","doi":"https://doi.org/10.1007/s00894-014-2283-8","mag":"2003191300","pmid":"https://pubmed.ncbi.nlm.nih.gov/24863533"},"language":"en","primary_location":{"id":"doi:10.1007/s00894-014-2283-8","doi":"https://doi.org/10.1007/s00894-014-2283-8","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s00894-014-2283-8","pdf_url":null,"source":{"id":"https://openalex.org/S113170167","display_name":"Journal of Molecular Modeling","issn_l":"0948-5023","issn":["0948-5023","1610-2940"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-d","jufo-1","medline","norway-1","poland-40","russia-white-list-2"],"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 Molecular Modeling","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"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/A5062342408","display_name":"Vinod Jani","orcid":"https://orcid.org/0000-0003-3049-0891","observed_orcids":["https://orcid.org/0000-0003-3049-0891"]},"institutions":[{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]},{"id":"https://openalex.org/I878213199","display_name":"Savitribai Phule Pune University","ror":"https://ror.org/044g6d731","country_code":"IN","type":"education","lineage":["https://openalex.org/I878213199"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Vinod Jani","raw_affiliation_strings":["Centre for Development of Advanced Computing, Pune University Campus Ganeshkhind, Pune, 411007, Maharashtra, India","Pune University Campus, Ganeshkhind"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Development of Advanced Computing, Pune University Campus Ganeshkhind, Pune, 411007, Maharashtra, India","institution_ids":["https://openalex.org/I1331500379","https://openalex.org/I878213199"]},{"raw_affiliation_string":"Pune University Campus, Ganeshkhind","institution_ids":["https://openalex.org/I878213199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043656057","display_name":"Uddhavesh Sonavane","orcid":"https://orcid.org/0000-0002-2482-9126","observed_orcids":["https://orcid.org/0000-0002-2482-9126"]},"institutions":[{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]},{"id":"https://openalex.org/I878213199","display_name":"Savitribai Phule Pune University","ror":"https://ror.org/044g6d731","country_code":"IN","type":"education","lineage":["https://openalex.org/I878213199"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Uddhavesh B. Sonavane","raw_affiliation_strings":["Centre for Development of Advanced Computing, Pune University Campus Ganeshkhind, Pune, 411007, Maharashtra, India","Pune University Campus, Ganeshkhind"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Development of Advanced Computing, Pune University Campus Ganeshkhind, Pune, 411007, Maharashtra, India","institution_ids":["https://openalex.org/I1331500379","https://openalex.org/I878213199"]},{"raw_affiliation_string":"Pune University Campus, Ganeshkhind","institution_ids":["https://openalex.org/I878213199"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041136744","display_name":"Rajendra Joshi","orcid":"https://orcid.org/0000-0003-1299-0091","observed_orcids":["https://orcid.org/0000-0003-1299-0091"]},"institutions":[{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]},{"id":"https://openalex.org/I878213199","display_name":"Savitribai Phule Pune University","ror":"https://ror.org/044g6d731","country_code":"IN","type":"education","lineage":["https://openalex.org/I878213199"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Rajendra Joshi","raw_affiliation_strings":["Centre for Development of Advanced Computing, Pune University Campus Ganeshkhind, Pune, 411007, Maharashtra, India","Pune University Campus, Ganeshkhind"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Development of Advanced Computing, Pune University Campus Ganeshkhind, Pune, 411007, Maharashtra, India","institution_ids":["https://openalex.org/I1331500379","https://openalex.org/I878213199"]},{"raw_affiliation_string":"Pune University Campus, Ganeshkhind","institution_ids":["https://openalex.org/I878213199"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5041136744"],"corresponding_institution_ids":["https://openalex.org/I1331500379","https://openalex.org/I878213199"],"apc_list":{"value":4290,"currency":"USD","value_usd":4290},"apc_paid":null,"fwci":0.5508,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.60011965,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"20","issue":"6","first_page":"2283","last_page":"2283"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.0,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.0,"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/engrailed-homeodomain","display_name":"engrailed homeodomain","score":0.9860000014305115},{"id":"https://openalex.org/keywords/protein-folding","display_name":"protein folding","score":0.8169999718666077},{"id":"https://openalex.org/keywords/folding-intermediates","display_name":"folding intermediates","score":0.824999988079071},{"id":"https://openalex.org/keywords/folding-funnel","display_name":"folding funnel","score":0.8849999904632568},{"id":"https://openalex.org/keywords/replica-exchange-molecular-dynamics","display_name":"replica exchange molecular dynamics","score":0.9359999895095825},{"id":"https://openalex.org/keywords/umbrella-sampling","display_name":"umbrella sampling","score":0.9919999837875366},{"id":"https://openalex.org/keywords/free-energy-analysis","display_name":"free energy analysis","score":0.6579999923706055},{"id":"https://openalex.org/keywords/protein-engineering","display_name":"protein engineering","score":0.6389999985694885}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7134756445884705},{"id":"https://openalex.org/C128747166","wikidata":"https://www.wikidata.org/wiki/Q7881414","display_name":"Umbrella sampling","level":3,"score":0.6767348051071167},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.581336259841919},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.5365403294563293},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.46123480796813965},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3830035626888275},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.38125085830688477},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32847726345062256},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.23474401235580444},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14023423194885254},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09395676851272583},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06436094641685486},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/s00894-014-2283-8","doi":"https://doi.org/10.1007/s00894-014-2283-8","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s00894-014-2283-8","pdf_url":null,"source":{"id":"https://openalex.org/S113170167","display_name":"Journal of Molecular Modeling","issn_l":"0948-5023","issn":["0948-5023","1610-2940"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-d","jufo-1","medline","norway-1","poland-40","russia-white-list-2"],"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 Molecular Modeling","raw_type":"journal-article"},{"id":"pmid:24863533","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24863533","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":"Journal of molecular modeling","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W1964340681","https://openalex.org/W1964758803","https://openalex.org/W1966743338","https://openalex.org/W1969204825","https://openalex.org/W1976528962","https://openalex.org/W1980933072","https://openalex.org/W1981385422","https://openalex.org/W1981781995","https://openalex.org/W1982092510","https://openalex.org/W1990593157","https://openalex.org/W1993177346","https://openalex.org/W1996051469","https://openalex.org/W1996129910","https://openalex.org/W2004461664","https://openalex.org/W2004822259","https://openalex.org/W2006520052","https://openalex.org/W2009513422","https://openalex.org/W2009929688","https://openalex.org/W2014095962","https://openalex.org/W2016858252","https://openalex.org/W2018312454","https://openalex.org/W2021002797","https://openalex.org/W2029313276","https://openalex.org/W2029871341","https://openalex.org/W2030955117","https://openalex.org/W2031016294","https://openalex.org/W2039740672","https://openalex.org/W2040108920","https://openalex.org/W2040809566","https://openalex.org/W2045418085","https://openalex.org/W2045777307","https://openalex.org/W2046290651","https://openalex.org/W2059490112","https://openalex.org/W2063254501","https://openalex.org/W2063653675","https://openalex.org/W2070458820","https://openalex.org/W2072429249","https://openalex.org/W2072746162","https://openalex.org/W2088780328","https://openalex.org/W2092219016","https://openalex.org/W2092356013","https://openalex.org/W2092388962","https://openalex.org/W2098106418","https://openalex.org/W2101348065","https://openalex.org/W2112154906","https://openalex.org/W2112985723","https://openalex.org/W2117897850","https://openalex.org/W2120894980","https://openalex.org/W2126677658","https://openalex.org/W2143058551","https://openalex.org/W2154794547","https://openalex.org/W2157504720","https://openalex.org/W2158476854","https://openalex.org/W2160721947","https://openalex.org/W2311078281","https://openalex.org/W2312256105"],"related_works":["https://openalex.org/W2063254501","https://openalex.org/W149235922","https://openalex.org/W2409073222","https://openalex.org/W2120894980","https://openalex.org/W1981781995","https://openalex.org/W2022951267","https://openalex.org/W1977045830","https://openalex.org/W7074061154","https://openalex.org/W1977981911","https://openalex.org/W2032311486"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-25T07:29:55.448023","created_date":"2016-06-24T00:00:00"}
