{"id":"https://openalex.org/W1501591636","doi":"https://doi.org/10.3233/isb-2009-0385","title":"In silico Analysis of Evolutionary Patterns in Restriction Endonucleases","display_name":"In silico Analysis of Evolutionary Patterns in Restriction Endonucleases","publication_year":2009,"publication_date":"2009-01-01","ids":{"openalex":"https://openalex.org/W1501591636","doi":"https://doi.org/10.3233/isb-2009-0385","mag":"1501591636","pmid":"https://pubmed.ncbi.nlm.nih.gov/19537161"},"language":"en","primary_location":{"id":"doi:10.3233/isb-2009-0385","is_oa":false,"landing_page_url":"https://doi.org/10.3233/isb-2009-0385","pdf_url":null,"source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation","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/A5011110357","display_name":"Tiratha Raj Singh","orcid":"https://orcid.org/0000-0003-1109-5626"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]},{"id":"https://openalex.org/I91277730","display_name":"Maulana Azad National Institute of Technology","ror":"https://ror.org/026vtd268","country_code":"IN","type":"education","lineage":["https://openalex.org/I91277730"]}],"countries":["IL","IN"],"is_corresponding":true,"raw_author_name":"Tiratha Raj Singh","raw_affiliation_strings":["Department of Bioinformatics, Maulana Azad National\r\t\t\t Institute of Technology (MANIT), Bhopal, India","Department of Zoology, Faculty of life Sciences,\r\t\t\t Tel-Aviv University, Tel-Aviv, Israel","Department of Bioinformatics, Maulana Azad National Institute of Technology (MANIT), Bhopal, India","Department of Zoology, Faculty of life Sciences, Tel-Aviv University, Tel-Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Maulana Azad National\r\t\t\t Institute of Technology (MANIT), Bhopal, India","institution_ids":["https://openalex.org/I91277730"]},{"raw_affiliation_string":"Department of Zoology, Faculty of life Sciences,\r\t\t\t Tel-Aviv University, Tel-Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Department of Bioinformatics, Maulana Azad National Institute of Technology (MANIT), Bhopal, India","institution_ids":["https://openalex.org/I91277730"]},{"raw_affiliation_string":"Department of Zoology, Faculty of life Sciences, Tel-Aviv University, Tel-Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026452888","display_name":"Kamal Raj Pardasani","orcid":"https://orcid.org/0000-0002-0256-7217"},"institutions":[{"id":"https://openalex.org/I91277730","display_name":"Maulana Azad National Institute of Technology","ror":"https://ror.org/026vtd268","country_code":"IN","type":"education","lineage":["https://openalex.org/I91277730"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Kamal Raj Pardasani","raw_affiliation_strings":["Department of Mathematics, Maulana Azad National\r\t\t\t Institute of Technology (MANIT), Bhopal, India","Department of Mathematics, Maulana Azad National Institute of Technology (MANIT), Bhopal, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Maulana Azad National\r\t\t\t Institute of Technology (MANIT), Bhopal, India","institution_ids":["https://openalex.org/I91277730"]},{"raw_affiliation_string":"Department of Mathematics, Maulana Azad National Institute of Technology (MANIT), Bhopal, India","institution_ids":["https://openalex.org/I91277730"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5011110357"],"corresponding_institution_ids":["https://openalex.org/I16391192","https://openalex.org/I91277730"],"apc_list":null,"apc_paid":null,"fwci":0.1369,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.5252247,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"9","issue":"1-2","first_page":"45","last_page":"53"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9997000098228455,"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":0.9997000098228455,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.9984999895095825,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/restriction-enzyme","display_name":"Restriction enzyme","score":0.9098730087280273},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6165341138839722},{"id":"https://openalex.org/keywords/restriction-site","display_name":"Restriction site","score":0.6146601438522339},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6122222542762756},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5871037244796753},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5383815169334412},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5145913362503052},{"id":"https://openalex.org/keywords/cleave","display_name":"Cleave","score":0.49764159321784973},{"id":"https://openalex.org/keywords/nuclease","display_name":"Nuclease","score":0.4607914388179779},{"id":"https://openalex.org/keywords/endonuclease","display_name":"Endonuclease","score":0.4127758741378784},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2621830999851227}],"concepts":[{"id":"https://openalex.org/C128319531","wikidata":"https://www.wikidata.org/wiki/Q219715","display_name":"Restriction enzyme","level":3,"score":0.9098730087280273},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6165341138839722},{"id":"https://openalex.org/C58301748","wikidata":"https://www.wikidata.org/wiki/Q1074969","display_name":"Restriction site","level":4,"score":0.6146601438522339},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6122222542762756},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5871037244796753},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5383815169334412},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5145913362503052},{"id":"https://openalex.org/C19014433","wikidata":"https://www.wikidata.org/wiki/Q5130995","display_name":"Cleave","level":3,"score":0.49764159321784973},{"id":"https://openalex.org/C2777271071","wikidata":"https://www.wikidata.org/wiki/Q422529","display_name":"Nuclease","level":3,"score":0.4607914388179779},{"id":"https://openalex.org/C2777028655","wikidata":"https://www.wikidata.org/wiki/Q415601","display_name":"Endonuclease","level":3,"score":0.4127758741378784},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2621830999851227}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004262","descriptor_name":"DNA Restriction Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004262","descriptor_name":"DNA Restriction Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004262","descriptor_name":"DNA Restriction Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004262","descriptor_name":"DNA Restriction Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004262","descriptor_name":"DNA Restriction Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004262","descriptor_name":"DNA Restriction Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004262","descriptor_name":"DNA Restriction Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004262","descriptor_name":"DNA Restriction Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004262","descriptor_name":"DNA Restriction Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.3233/isb-2009-0385","is_oa":false,"landing_page_url":"https://doi.org/10.3233/isb-2009-0385","pdf_url":null,"source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation","raw_type":"journal-article"},{"id":"pmid:19537161","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19537161","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":"In silico biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6899999976158142,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W34915411","https://openalex.org/W1506010125","https://openalex.org/W1545338345","https://openalex.org/W1586342495","https://openalex.org/W1906939693","https://openalex.org/W1963534925","https://openalex.org/W1964143460","https://openalex.org/W1966041739","https://openalex.org/W1971330126","https://openalex.org/W1987309203","https://openalex.org/W2015642465","https://openalex.org/W2021466856","https://openalex.org/W2022058405","https://openalex.org/W2025104601","https://openalex.org/W2030748296","https://openalex.org/W2036634847","https://openalex.org/W2037412273","https://openalex.org/W2041076979","https://openalex.org/W2069663555","https://openalex.org/W2070196801","https://openalex.org/W2080698851","https://openalex.org/W2089859866","https://openalex.org/W2101421856","https://openalex.org/W2109375234","https://openalex.org/W2118473805","https://openalex.org/W2139348667","https://openalex.org/W2150297520","https://openalex.org/W2154833032"],"related_works":["https://openalex.org/W1967994784","https://openalex.org/W2416924244","https://openalex.org/W303221755","https://openalex.org/W761389014","https://openalex.org/W57272298","https://openalex.org/W1995987289","https://openalex.org/W2418350746","https://openalex.org/W2396146277","https://openalex.org/W2463738679","https://openalex.org/W2419380053"],"abstract_inverted_index":{"Restriction":[0,44,53],"endonucleases":[1,16,37,54,93,120],"represent":[2],"one":[3],"of":[4,9,20,40,145],"the":[5,25,146,159],"best":[6],"studied":[7],"examples":[8],"DNA":[10,22,109],"binding":[11],"proteins.":[12],"Type":[13,34],"II":[14,35,122],"restriction":[15,36,41,92,119],"recognize":[17],"short":[18],"sequences":[19,97],"foreign":[21],"and":[23,51,61,73,83,94,111,123,128,140],"cleave":[24],"target":[26],"on":[27],"both":[28],"strands":[29],"with":[30],"remarkable":[31],"sequence":[32],"specificity.":[33],"are":[38,55,64],"part":[39],"modification":[42,45],"systems.":[43],"systems":[46],"occur":[47],"ubiquitously":[48],"among":[49,86],"bacteria":[50],"archaea.":[52],"indispensable":[56],"tools":[57],"in":[58,102,118,166],"molecular":[59,141],"biology":[60],"biotechnology.":[62],"They":[63],"important":[65],"model":[66],"system":[67],"for":[68,79,138,158],"specific":[69],"protein-nucleic":[70],"acid":[71],"interactions":[72],"also":[74,150],"serve":[75],"as":[76],"good":[77],"example":[78],"investigating":[80],"structural,":[81,126],"functional":[82,127],"evolutionary":[84,129,156],"relationships":[85],"various":[87,116],"biomolecules.":[88],"The":[89],"interaction":[90],"between":[91],"their":[95,125],"recognition":[96],"plays":[98],"a":[99],"crucial":[100],"role":[101],"biochemical":[103],"activities":[104],"like":[105],"catalytic":[106],"site/metal":[107],"binding,":[108],"repair":[110],"recombination":[112],"etc.":[113],"We":[114],"study":[115],"patterns":[117,144],"type":[121],"analyzed":[124,152,160],"role.":[130],"Our":[131],"studies":[132],"support":[133],"X-ray":[134],"crystallographic":[135],"studies,":[136],"arguing":[137],"divergence":[139],"evolution.":[142],"Conservation":[143],"nuclease":[147],"superfamily":[148],"have":[149],"been":[151],"by":[153],"estimating":[154],"site-specific":[155],"rates":[157],"structures":[161],"related":[162],"to":[163],"respective":[164],"chains":[165],"this":[167],"study.":[168]},"counts_by_year":[{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}