{"id":"https://openalex.org/W2009298790","doi":"https://doi.org/10.1007/s10822-014-9767-6","title":"Analysis of stacking overlap in nucleic acid structures: algorithm and application","display_name":"Analysis of stacking overlap in nucleic acid structures: algorithm and application","publication_year":2014,"publication_date":"2014-07-02","ids":{"openalex":"https://openalex.org/W2009298790","doi":"https://doi.org/10.1007/s10822-014-9767-6","mag":"2009298790","pmid":"https://pubmed.ncbi.nlm.nih.gov/24990628"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-014-9767-6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-014-9767-6","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041249033","display_name":"Pavan Kumar Pingali","orcid":null},"institutions":[{"id":"https://openalex.org/I16019930","display_name":"Saha Institute of Nuclear Physics","ror":"https://ror.org/0491yz035","country_code":"IN","type":"facility","lineage":["https://openalex.org/I16019930"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Pavan Kumar Pingali","raw_affiliation_strings":["Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","Saha Institute of Nuclear Physics"],"affiliations":[{"raw_affiliation_string":"Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","institution_ids":["https://openalex.org/I16019930"]},{"raw_affiliation_string":"Saha Institute of Nuclear Physics","institution_ids":["https://openalex.org/I16019930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012318444","display_name":"Sukanya Halder","orcid":null},"institutions":[{"id":"https://openalex.org/I16019930","display_name":"Saha Institute of Nuclear Physics","ror":"https://ror.org/0491yz035","country_code":"IN","type":"facility","lineage":["https://openalex.org/I16019930"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sukanya Halder","raw_affiliation_strings":["Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","Saha Institute of Nuclear Physics"],"affiliations":[{"raw_affiliation_string":"Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","institution_ids":["https://openalex.org/I16019930"]},{"raw_affiliation_string":"Saha Institute of Nuclear Physics","institution_ids":["https://openalex.org/I16019930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062127191","display_name":"Debasish Mukherjee","orcid":"https://orcid.org/0000-0002-0158-0700"},"institutions":[{"id":"https://openalex.org/I16019930","display_name":"Saha Institute of Nuclear Physics","ror":"https://ror.org/0491yz035","country_code":"IN","type":"facility","lineage":["https://openalex.org/I16019930"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Debasish Mukherjee","raw_affiliation_strings":["Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","Saha Institute of Nuclear Physics"],"affiliations":[{"raw_affiliation_string":"Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","institution_ids":["https://openalex.org/I16019930"]},{"raw_affiliation_string":"Saha Institute of Nuclear Physics","institution_ids":["https://openalex.org/I16019930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054921936","display_name":"Sankar Basu","orcid":"https://orcid.org/0000-0003-1393-1982"},"institutions":[{"id":"https://openalex.org/I16019930","display_name":"Saha Institute of Nuclear Physics","ror":"https://ror.org/0491yz035","country_code":"IN","type":"facility","lineage":["https://openalex.org/I16019930"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sankar Basu","raw_affiliation_strings":["Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","Saha Institute of Nuclear Physics"],"affiliations":[{"raw_affiliation_string":"Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","institution_ids":["https://openalex.org/I16019930"]},{"raw_affiliation_string":"Saha Institute of Nuclear Physics","institution_ids":["https://openalex.org/I16019930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103243030","display_name":"Rahul Banerjee","orcid":"https://orcid.org/0000-0002-8935-0765"},"institutions":[{"id":"https://openalex.org/I16019930","display_name":"Saha Institute of Nuclear Physics","ror":"https://ror.org/0491yz035","country_code":"IN","type":"facility","lineage":["https://openalex.org/I16019930"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Rahul Banerjee","raw_affiliation_strings":["Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","Saha Institute of Nuclear Physics"],"affiliations":[{"raw_affiliation_string":"Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","institution_ids":["https://openalex.org/I16019930"]},{"raw_affiliation_string":"Saha Institute of Nuclear Physics","institution_ids":["https://openalex.org/I16019930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036565022","display_name":"Devapriya Choudhury","orcid":"https://orcid.org/0000-0001-6779-9425"},"institutions":[{"id":"https://openalex.org/I152429107","display_name":"Jawaharlal Nehru University","ror":"https://ror.org/0567v8t28","country_code":"IN","type":"education","lineage":["https://openalex.org/I152429107"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Devapriya Choudhury","raw_affiliation_strings":["School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India","Jawaharlal Nehru University#TAB#"],"affiliations":[{"raw_affiliation_string":"School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India","institution_ids":["https://openalex.org/I152429107"]},{"raw_affiliation_string":"Jawaharlal Nehru University#TAB#","institution_ids":["https://openalex.org/I152429107"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051389777","display_name":"Dhananjay Bhattacharyya","orcid":"https://orcid.org/0000-0001-9227-6490"},"institutions":[{"id":"https://openalex.org/I16019930","display_name":"Saha Institute of Nuclear Physics","ror":"https://ror.org/0491yz035","country_code":"IN","type":"facility","lineage":["https://openalex.org/I16019930"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Dhananjay Bhattacharyya","raw_affiliation_strings":["Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","Saha Institute of Nuclear Physics"],"affiliations":[{"raw_affiliation_string":"Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India","institution_ids":["https://openalex.org/I16019930"]},{"raw_affiliation_string":"Saha Institute of Nuclear Physics","institution_ids":["https://openalex.org/I16019930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5041249033"],"corresponding_institution_ids":["https://openalex.org/I16019930"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":1.5638,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.82141553,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"28","issue":"8","first_page":"851","last_page":"867"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9976000189781189,"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/stacking","display_name":"Stacking","score":0.8461718559265137},{"id":"https://openalex.org/keywords/nucleic-acid","display_name":"Nucleic acid","score":0.6901723146438599},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5483952760696411},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5382959246635437},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33864057064056396},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.22774797677993774},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1582472324371338},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07213667035102844}],"concepts":[{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.8461718559265137},{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.6901723146438599},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5483952760696411},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5382959246635437},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33864057064056396},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.22774797677993774},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1582472324371338},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07213667035102844},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-014-9767-6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-014-9767-6","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:24990628","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24990628","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of computer-aided molecular design","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310071","display_name":"Indian Institute of Science","ror":"https://ror.org/04dese585"},{"id":"https://openalex.org/F4320312060","display_name":"Francis Crick Institute","ror":"https://ror.org/04tnbqb63"},{"id":"https://openalex.org/F4320318735","display_name":"National Institute of Pharmaceutical Education and Research, Ahmedabad","ror":"https://ror.org/04t67vr60"},{"id":"https://openalex.org/F4320327905","display_name":"National Institute of Science Education and Research","ror":"https://ror.org/02r2k1c68"},{"id":"https://openalex.org/F4320330981","display_name":"National Institute of Pharmaceutical Education and Research, Raebareli","ror":"https://ror.org/025qtp564"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":66,"referenced_works":["https://openalex.org/W607795070","https://openalex.org/W962838231","https://openalex.org/W1484535432","https://openalex.org/W1651872625","https://openalex.org/W1839579164","https://openalex.org/W1970634015","https://openalex.org/W1980453179","https://openalex.org/W1980633583","https://openalex.org/W1980722147","https://openalex.org/W1982404448","https://openalex.org/W1982680051","https://openalex.org/W1984543894","https://openalex.org/W1985124981","https://openalex.org/W1985606769","https://openalex.org/W1988380385","https://openalex.org/W1990641854","https://openalex.org/W1999491344","https://openalex.org/W2003122343","https://openalex.org/W2006640104","https://openalex.org/W2009555898","https://openalex.org/W2012268010","https://openalex.org/W2012813328","https://openalex.org/W2018387876","https://openalex.org/W2018559377","https://openalex.org/W2019991838","https://openalex.org/W2025529107","https://openalex.org/W2026486846","https://openalex.org/W2047048575","https://openalex.org/W2047766036","https://openalex.org/W2049210474","https://openalex.org/W2053561906","https://openalex.org/W2055317682","https://openalex.org/W2062516618","https://openalex.org/W2063675437","https://openalex.org/W2066906496","https://openalex.org/W2067249172","https://openalex.org/W2070679144","https://openalex.org/W2072925380","https://openalex.org/W2082442609","https://openalex.org/W2085616298","https://openalex.org/W2086108686","https://openalex.org/W2086968914","https://openalex.org/W2096184392","https://openalex.org/W2100380699","https://openalex.org/W2102980378","https://openalex.org/W2106096530","https://openalex.org/W2106246926","https://openalex.org/W2106478835","https://openalex.org/W2107533804","https://openalex.org/W2121418783","https://openalex.org/W2122199548","https://openalex.org/W2127382372","https://openalex.org/W2130479394","https://openalex.org/W2142393243","https://openalex.org/W2142455569","https://openalex.org/W2150404344","https://openalex.org/W2155361333","https://openalex.org/W2156909690","https://openalex.org/W2161968806","https://openalex.org/W2162548786","https://openalex.org/W2167120376","https://openalex.org/W2171089873","https://openalex.org/W2172010381","https://openalex.org/W2319770548","https://openalex.org/W2334105408","https://openalex.org/W4230118546"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2035329725","https://openalex.org/W4376641153","https://openalex.org/W2050788868","https://openalex.org/W2070875936","https://openalex.org/W4250391473","https://openalex.org/W3045075405","https://openalex.org/W4302292679","https://openalex.org/W2956222435","https://openalex.org/W4241625287"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}