{"id":"https://openalex.org/W4239660924","doi":"https://doi.org/10.1142/s0219720010004811","title":"DEPPDB \u2014 DNA ELECTROSTATIC POTENTIAL PROPERTIES DATABASE: ELECTROSTATIC PROPERTIES OF GENOME DNA","display_name":"DEPPDB \u2014 DNA ELECTROSTATIC POTENTIAL PROPERTIES DATABASE: ELECTROSTATIC PROPERTIES OF GENOME DNA","publication_year":2010,"publication_date":"2010-03-23","ids":{"openalex":"https://openalex.org/W4239660924","doi":"https://doi.org/10.1142/s0219720010004811","pmid":"https://pubmed.ncbi.nlm.nih.gov/20556853"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720010004811","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720010004811","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5111436774","display_name":"Alexander A. Osypov","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155801","display_name":"Institute of Cell Biophysics","ror":"https://ror.org/05gbnpz65","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210155801"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"ALEXANDER A. OSYPOV","raw_affiliation_strings":["Laboratory of Mechanisms of the Cell Genome Functioning, Institute of Cell Biophysics RAS, Pushchino, 142290, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Mechanisms of the Cell Genome Functioning, Institute of Cell Biophysics RAS, Pushchino, 142290, Russia","institution_ids":["https://openalex.org/I4210155801"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025898914","display_name":"Gleb G. Krutinin","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155801","display_name":"Institute of Cell Biophysics","ror":"https://ror.org/05gbnpz65","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210155801"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"GLEB G. KRUTININ","raw_affiliation_strings":["Laboratory of Mechanisms of the Cell Genome Functioning, Institute of Cell Biophysics RAS, Pushchino, 142290, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Mechanisms of the Cell Genome Functioning, Institute of Cell Biophysics RAS, Pushchino, 142290, Russia","institution_ids":["https://openalex.org/I4210155801"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027621989","display_name":"S. G. Kamzolova","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155801","display_name":"Institute of Cell Biophysics","ror":"https://ror.org/05gbnpz65","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210155801"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"SVETLANA G. KAMZOLOVA","raw_affiliation_strings":["Laboratory of Mechanisms of the Cell Genome Functioning, Institute of Cell Biophysics RAS, Pushchino, 142290, Russia"],"affiliations":[{"raw_affiliation_string":"Laboratory of Mechanisms of the Cell Genome Functioning, Institute of Cell Biophysics RAS, Pushchino, 142290, Russia","institution_ids":["https://openalex.org/I4210155801"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5111436774"],"corresponding_institution_ids":["https://openalex.org/I4210155801"],"apc_list":null,"apc_paid":null,"fwci":0.5287,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.66846346,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"08","issue":"03","first_page":"413","last_page":"425"},"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":0.9983999729156494,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9980000257492065,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7439648509025574},{"id":"https://openalex.org/keywords/refseq","display_name":"RefSeq","score":0.7235935926437378},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5996483564376831},{"id":"https://openalex.org/keywords/electrostatics","display_name":"Electrostatics","score":0.5634621381759644},{"id":"https://openalex.org/keywords/rna-polymerase","display_name":"RNA polymerase","score":0.52348792552948},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5027153491973877},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.4953981637954712},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4812590777873993},{"id":"https://openalex.org/keywords/polymerase","display_name":"Polymerase","score":0.4780562222003937},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.47148820757865906},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4174864590167999},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4170319437980652},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22320342063903809},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2106570303440094}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7439648509025574},{"id":"https://openalex.org/C151810110","wikidata":"https://www.wikidata.org/wiki/Q7307074","display_name":"RefSeq","level":4,"score":0.7235935926437378},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5996483564376831},{"id":"https://openalex.org/C117626034","wikidata":"https://www.wikidata.org/wiki/Q26336","display_name":"Electrostatics","level":2,"score":0.5634621381759644},{"id":"https://openalex.org/C2776449523","wikidata":"https://www.wikidata.org/wiki/Q272631","display_name":"RNA polymerase","level":4,"score":0.52348792552948},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5027153491973877},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4953981637954712},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4812590777873993},{"id":"https://openalex.org/C82381507","wikidata":"https://www.wikidata.org/wiki/Q416878","display_name":"Polymerase","level":3,"score":0.4780562222003937},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.47148820757865906},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4174864590167999},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4170319437980652},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22320342063903809},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2106570303440094},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"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":"Q000235","qualifier_name":"genetics","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":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012321","descriptor_name":"DNA-Directed RNA Polymerases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012321","descriptor_name":"DNA-Directed RNA Polymerases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012321","descriptor_name":"DNA-Directed RNA Polymerases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012321","descriptor_name":"DNA-Directed RNA Polymerases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012321","descriptor_name":"DNA-Directed RNA Polymerases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012321","descriptor_name":"DNA-Directed RNA Polymerases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720010004811","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720010004811","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:20556853","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20556853","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 bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334801","display_name":"Russian Academy of Sciences","ror":"https://ror.org/05qrfxd25"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1511196224","https://openalex.org/W1577972586","https://openalex.org/W1634884476","https://openalex.org/W1964007348","https://openalex.org/W1974916610","https://openalex.org/W1983764154","https://openalex.org/W1999220636","https://openalex.org/W2012627860","https://openalex.org/W2018300117","https://openalex.org/W2039859086","https://openalex.org/W2061799500","https://openalex.org/W2078636078","https://openalex.org/W2104730528","https://openalex.org/W2105089812","https://openalex.org/W2107903949","https://openalex.org/W2111400482","https://openalex.org/W2116060321","https://openalex.org/W2146135000","https://openalex.org/W2412727441","https://openalex.org/W4250297812"],"related_works":["https://openalex.org/W2970236921","https://openalex.org/W2048863389","https://openalex.org/W2138968083","https://openalex.org/W909712953","https://openalex.org/W1838655642","https://openalex.org/W1994181332","https://openalex.org/W3185267093","https://openalex.org/W2023767520","https://openalex.org/W2389717545","https://openalex.org/W2784218872"],"abstract_inverted_index":{"The":[0],"electrostatic":[1,35,88,148,196],"properties":[2,36,50,83,146],"of":[3,16,37,46,51,84,93,126,142,165,173,176,186,194],"genome":[4,38,52,86],"DNA":[5,39,87],"influence":[6],"its":[7,42,94,121],"interactions":[8],"with":[9,41,101],"different":[10],"proteins,":[11],"in":[12,58,178],"particular,":[13],"the":[14,34,67,71,85,102,117,127,140,158,162,171,174,187,195],"regulation":[15],"transcription":[17],"by":[18],"RNA-polymerases.":[19],"DEPPDB--DNA":[20],"Electrostatic":[21],"Potential":[22],"Properties":[23],"Database--was":[24],"developed":[25],"to":[26,79,109,168,190],"hold":[27],"and":[28,44,48,54,75,91,112,120,132,147,161],"provide":[29],"all":[30,70],"available":[31],"information":[32],"on":[33,62,115],"combined":[40],"sequence":[43,118],"annotation":[45],"biological":[47],"structural":[49],"elements":[53],"whole":[55],"genomes.":[56],"Genomes":[57],"DEPPDB":[59],"are":[60,96],"organized":[61],"a":[63,137,154,183],"taxonomical":[64],"basis.":[65],"Currently,":[66],"database":[68],"contains":[69],"completely":[72],"sequenced":[73],"bacterial":[74,131],"viral":[76,133],"genomes":[77],"according":[78],"NCBI":[80],"RefSeq.":[81],"General":[82],"potential":[89,99,159],"profile":[90,149],"principles":[92],"formation":[95],"revealed.":[97],"This":[98,181],"correlates":[100],"GC":[103],"content":[104],"but":[105],"does":[106],"not":[107],"correspond":[108],"it":[110],"exactly":[111],"strongly":[113],"depends":[114],"both":[116],"arrangement":[119],"context":[122],"(flanking":[123],"regions).":[124],"Analysis":[125],"promoter":[128,188],"regions":[129,189],"for":[130],"RNA":[134,166],"polymerases":[135],"revealed":[136],"correspondence":[138],"between":[139,157],"scale":[141],"these":[143,179],"proteins'":[144],"physical":[145],"patterns.":[150],"We":[151],"also":[152],"discovered":[153],"direct":[155],"correlation":[156],"value":[160],"binding":[163],"frequency":[164],"polymerase":[167],"DNA,":[169],"supporting":[170],"idea":[172],"role":[175],"electrostatics":[177],"interactions.":[180],"matches":[182],"pronounced":[184],"tendency":[185],"possess":[191],"higher":[192],"values":[193],"potential.":[197]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2018,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":7},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}