SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets
Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly growing infectious disease, widely spread with high mortality rates. Since the release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discove...
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| Veröffentlicht in: | Briefings in bioinformatics 2021-03, Vol.22 (2), p.769-780 |
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| creator | Alsulami, Ali F Thomas, Sherine E Jamasb, Arian R Beaudoin, Christopher A Moghul, Ismail Bannerman, Bridget Copoiu, Liviu Vedithi, Sundeep Chaitanya Torres, Pedro Blundell, Tom L |
| description | Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly growing infectious disease, widely spread with high mortality rates. Since the release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discovery, which also requires knowledge of the 3D structure of the proteome. Where there are no experimentally solved structures, our group has created 3D models with coverage of 97.5% and characterized them using state-of-the-art computational approaches. Models of protomers and oligomers, together with predictions of substrate and allosteric binding sites, protein-ligand docking, SARS-CoV-2 protein interactions with human proteins, impacts of mutations, and mapped solved experimental structures are freely available for download. These are implemented in SARS CoV-2 3D, a comprehensive and user-friendly database, available at https://sars3d.com/. This provides essential information for drug discovery, both to evaluate targets and design new potential therapeutics. |
| doi_str_mv | 10.1093/bib/bbaa404 |
| format | Article |
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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly growing infectious disease, widely spread with high mortality rates. Since the release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discovery, which also requires knowledge of the 3D structure of the proteome. Where there are no experimentally solved structures, our group has created 3D models with coverage of 97.5% and characterized them using state-of-the-art computational approaches. Models of protomers and oligomers, together with predictions of substrate and allosteric binding sites, protein-ligand docking, SARS-CoV-2 protein interactions with human proteins, impacts of mutations, and mapped solved experimental structures are freely available for download. These are implemented in SARS CoV-2 3D, a comprehensive and user-friendly database, available at https://sars3d.com/. This provides essential information for drug discovery, both to evaluate targets and design new potential therapeutics.</description><identifier>ISSN: 1467-5463</identifier><identifier>EISSN: 1477-4054</identifier><identifier>DOI: 10.1093/bib/bbaa404</identifier><identifier>PMID: 33416848</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Allosteric properties ; Antiviral Agents - pharmacology ; Binding sites ; Computer applications ; Coronaviruses ; COVID-19 - virology ; Databases, Protein ; Drug Delivery Systems ; Drug development ; Drug discovery ; Genomes ; Humans ; Infectious diseases ; Mutation ; Nucleotide sequence ; Oligomers ; Problem Solving Protocol ; Protein interaction ; Proteins ; Proteome ; Proteomes ; SARS-CoV-2 - drug effects ; SARS-CoV-2 - isolation & purification ; Severe acute respiratory syndrome ; Severe acute respiratory syndrome coronavirus 2 ; Substrates ; Therapeutic targets ; Three dimensional models ; Viral diseases</subject><ispartof>Briefings in bioinformatics, 2021-03, Vol.22 (2), p.769-780</ispartof><rights>The Author(s) 2021. Published by Oxford University Press. 2021</rights><rights>The Author(s) 2021. Published by Oxford University Press.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c440t-a7244cb4c925d079792229492b042c64dba84c49b2d47c948159ffaae97cb2f13</citedby><cites>FETCH-LOGICAL-c440t-a7244cb4c925d079792229492b042c64dba84c49b2d47c948159ffaae97cb2f13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7929435/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7929435/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,882,1599,27905,27906,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33416848$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Alsulami, Ali F</creatorcontrib><creatorcontrib>Thomas, Sherine E</creatorcontrib><creatorcontrib>Jamasb, Arian R</creatorcontrib><creatorcontrib>Beaudoin, Christopher A</creatorcontrib><creatorcontrib>Moghul, Ismail</creatorcontrib><creatorcontrib>Bannerman, Bridget</creatorcontrib><creatorcontrib>Copoiu, Liviu</creatorcontrib><creatorcontrib>Vedithi, Sundeep Chaitanya</creatorcontrib><creatorcontrib>Torres, Pedro</creatorcontrib><creatorcontrib>Blundell, Tom L</creatorcontrib><title>SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets</title><title>Briefings in bioinformatics</title><addtitle>Brief Bioinform</addtitle><description>Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly growing infectious disease, widely spread with high mortality rates. Since the release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discovery, which also requires knowledge of the 3D structure of the proteome. Where there are no experimentally solved structures, our group has created 3D models with coverage of 97.5% and characterized them using state-of-the-art computational approaches. Models of protomers and oligomers, together with predictions of substrate and allosteric binding sites, protein-ligand docking, SARS-CoV-2 protein interactions with human proteins, impacts of mutations, and mapped solved experimental structures are freely available for download. These are implemented in SARS CoV-2 3D, a comprehensive and user-friendly database, available at https://sars3d.com/. This provides essential information for drug discovery, both to evaluate targets and design new potential therapeutics.</description><subject>Allosteric properties</subject><subject>Antiviral Agents - pharmacology</subject><subject>Binding sites</subject><subject>Computer applications</subject><subject>Coronaviruses</subject><subject>COVID-19 - virology</subject><subject>Databases, Protein</subject><subject>Drug Delivery Systems</subject><subject>Drug development</subject><subject>Drug discovery</subject><subject>Genomes</subject><subject>Humans</subject><subject>Infectious diseases</subject><subject>Mutation</subject><subject>Nucleotide sequence</subject><subject>Oligomers</subject><subject>Problem Solving Protocol</subject><subject>Protein interaction</subject><subject>Proteins</subject><subject>Proteome</subject><subject>Proteomes</subject><subject>SARS-CoV-2 - drug effects</subject><subject>SARS-CoV-2 - isolation & purification</subject><subject>Severe acute respiratory syndrome</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Substrates</subject><subject>Therapeutic targets</subject><subject>Three dimensional models</subject><subject>Viral diseases</subject><issn>1467-5463</issn><issn>1477-4054</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kc1r3DAQxUVoSDbbnnovgkIvwYksjy2rh0LYfEIgkLS9ipEs73rZtRxJXsh_Hy27Dc0lpxmY37x5wyPka87OciaLc93pc60RgcEBmeQgRAashE_bvhJZCVVxTE5CWDLGmajzI3JcFJBXNdQTYp4uHp-ymfubcVpc0gYjagz2Jx37xvoQsW-6fk7jwlLjvOtx0_kx0MG7aN3a0jSndoOrEeOWG1wInV5Z2vgxbaGf2xg-k8MWV8F-2dcp-XN99Xt2m90_3NzNLu4zA8BihoIDGA1G8rJhQgrJOZcguWbATQWNxhoMSM0bEEZCnZeybRGtFEbzNi-m5NdOdxj12jbG9tHjSg2-W6N_UQ479X7Sdws1dxuVLkkoyiTwfS_g3fNoQ1RLN_o-eVa85FJWouBb6nRHGZ--9bZ9u5AztU1EpUTUPpFEf_vf1Bv7L4IE_NgBbhw-VHoFALSVuw</recordid><startdate>20210322</startdate><enddate>20210322</enddate><creator>Alsulami, Ali F</creator><creator>Thomas, Sherine E</creator><creator>Jamasb, Arian R</creator><creator>Beaudoin, Christopher A</creator><creator>Moghul, Ismail</creator><creator>Bannerman, Bridget</creator><creator>Copoiu, Liviu</creator><creator>Vedithi, Sundeep Chaitanya</creator><creator>Torres, Pedro</creator><creator>Blundell, Tom L</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7SC</scope><scope>8FD</scope><scope>FR3</scope><scope>JQ2</scope><scope>K9.</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20210322</creationdate><title>SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets</title><author>Alsulami, Ali F ; Thomas, Sherine E ; Jamasb, Arian R ; Beaudoin, Christopher A ; Moghul, Ismail ; Bannerman, Bridget ; Copoiu, Liviu ; Vedithi, Sundeep Chaitanya ; Torres, Pedro ; Blundell, Tom L</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c440t-a7244cb4c925d079792229492b042c64dba84c49b2d47c948159ffaae97cb2f13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Allosteric properties</topic><topic>Antiviral Agents - pharmacology</topic><topic>Binding sites</topic><topic>Computer applications</topic><topic>Coronaviruses</topic><topic>COVID-19 - virology</topic><topic>Databases, Protein</topic><topic>Drug Delivery Systems</topic><topic>Drug development</topic><topic>Drug discovery</topic><topic>Genomes</topic><topic>Humans</topic><topic>Infectious diseases</topic><topic>Mutation</topic><topic>Nucleotide sequence</topic><topic>Oligomers</topic><topic>Problem Solving Protocol</topic><topic>Protein interaction</topic><topic>Proteins</topic><topic>Proteome</topic><topic>Proteomes</topic><topic>SARS-CoV-2 - drug effects</topic><topic>SARS-CoV-2 - isolation & purification</topic><topic>Severe acute respiratory syndrome</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Substrates</topic><topic>Therapeutic targets</topic><topic>Three dimensional models</topic><topic>Viral diseases</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Alsulami, Ali F</creatorcontrib><creatorcontrib>Thomas, Sherine E</creatorcontrib><creatorcontrib>Jamasb, Arian R</creatorcontrib><creatorcontrib>Beaudoin, Christopher A</creatorcontrib><creatorcontrib>Moghul, Ismail</creatorcontrib><creatorcontrib>Bannerman, Bridget</creatorcontrib><creatorcontrib>Copoiu, Liviu</creatorcontrib><creatorcontrib>Vedithi, Sundeep Chaitanya</creatorcontrib><creatorcontrib>Torres, Pedro</creatorcontrib><creatorcontrib>Blundell, Tom L</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Briefings in bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Alsulami, Ali F</au><au>Thomas, Sherine E</au><au>Jamasb, Arian R</au><au>Beaudoin, Christopher A</au><au>Moghul, Ismail</au><au>Bannerman, Bridget</au><au>Copoiu, Liviu</au><au>Vedithi, Sundeep Chaitanya</au><au>Torres, Pedro</au><au>Blundell, Tom L</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets</atitle><jtitle>Briefings in bioinformatics</jtitle><addtitle>Brief Bioinform</addtitle><date>2021-03-22</date><risdate>2021</risdate><volume>22</volume><issue>2</issue><spage>769</spage><epage>780</epage><pages>769-780</pages><issn>1467-5463</issn><eissn>1477-4054</eissn><abstract>Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly growing infectious disease, widely spread with high mortality rates. Since the release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discovery, which also requires knowledge of the 3D structure of the proteome. Where there are no experimentally solved structures, our group has created 3D models with coverage of 97.5% and characterized them using state-of-the-art computational approaches. Models of protomers and oligomers, together with predictions of substrate and allosteric binding sites, protein-ligand docking, SARS-CoV-2 protein interactions with human proteins, impacts of mutations, and mapped solved experimental structures are freely available for download. These are implemented in SARS CoV-2 3D, a comprehensive and user-friendly database, available at https://sars3d.com/. This provides essential information for drug discovery, both to evaluate targets and design new potential therapeutics.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>33416848</pmid><doi>10.1093/bib/bbaa404</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Briefings in bioinformatics, 2021-03, Vol.22 (2), p.769-780 |
| issn | 1467-5463 1477-4054 |
| language | eng |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Business Source Complete; Oxford Journals Open Access Collection; PubMed Central |
| subjects | Allosteric properties Antiviral Agents - pharmacology Binding sites Computer applications Coronaviruses COVID-19 - virology Databases, Protein Drug Delivery Systems Drug development Drug discovery Genomes Humans Infectious diseases Mutation Nucleotide sequence Oligomers Problem Solving Protocol Protein interaction Proteins Proteome Proteomes SARS-CoV-2 - drug effects SARS-CoV-2 - isolation & purification Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Substrates Therapeutic targets Three dimensional models Viral diseases |
| title | SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets |
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