CoagVDb: a comprehensive database for coagulation factors and their associated SAPs

The current state of the art in medical genetics is to identify and classify the functional (deleterious) or non-functional (neutral) single amino acid substitutions (SAPs), also known as non-synonymous SNPs (nsSNPs). The primary goal is to elucidate the mechanisms through which functional SAPs exer...

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Autores principales:	Ali,Shabana Kouser, George Priya Doss,C, Thirumal Kumar,D, Zhu,Hailong
Lenguaje:	English
Publicado:	Sociedad de Biología de Chile 2015
Materias:	Coagulation cascade pathway Coagulation factor proteins Single amino acid substitutions SIFT PolyPhen 2 I-Mutant 3 Fathmm Align GVGD PhD-SNP SNPs& GO SNAP
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602015000100035
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spelling	oai:scielo:S0716-976020150001000352016-02-16CoagVDb: a comprehensive database for coagulation factors and their associated SAPsAli,Shabana KouserGeorge Priya Doss,CThirumal Kumar,DZhu,Hailong Coagulation cascade pathway Coagulation factor proteins Single amino acid substitutions SIFT PolyPhen 2 I-Mutant 3 Fathmm Align GVGD PhD-SNP SNPs& GO SNAP The current state of the art in medical genetics is to identify and classify the functional (deleterious) or non-functional (neutral) single amino acid substitutions (SAPs), also known as non-synonymous SNPs (nsSNPs). The primary goal is to elucidate the mechanisms through which functional SAPs exert their effects, and ultimately interrogating this information for association with complex phenotypes. This work focuses on coagulation factors involved in the coagulation cascade pathway which plays a vital role in the maintenance of homeostasis in the human system. We developed an integrated coagulation variation database, CoagVDb, which makes use of the biological information from various public databases such as NCBI, OMIM, UniProt, PDB and SAPs (rsIDs/variant). CoagVDb enriched with computational prediction scores classify SAPs as either deleterious or tolerated. Also, various other properties are incorporated such as amino acid composition, secondary structure elements, solvent accessibility, ordered/disordered regions, conservation, and the presence of disulfide bonds. This specialized database provides integration of various prediction scores from different computational methods along with gene, protein, and disease information. We hope our database will act as a useful reference resource for hematologists to reveal protein structure-function relationship and disease genotype-phenotype correlation.info:eu-repo/semantics/openAccessSociedad de Biología de ChileBiological Research v.48 20152015-01-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602015000100035en10.1186S/40659-015-0028-5
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Coagulation cascade pathway Coagulation factor proteins Single amino acid substitutions SIFT PolyPhen 2 I-Mutant 3 Fathmm Align GVGD PhD-SNP SNPs& GO SNAP
spellingShingle	Coagulation cascade pathway Coagulation factor proteins Single amino acid substitutions SIFT PolyPhen 2 I-Mutant 3 Fathmm Align GVGD PhD-SNP SNPs& GO SNAP Ali,Shabana Kouser George Priya Doss,C Thirumal Kumar,D Zhu,Hailong CoagVDb: a comprehensive database for coagulation factors and their associated SAPs
description	The current state of the art in medical genetics is to identify and classify the functional (deleterious) or non-functional (neutral) single amino acid substitutions (SAPs), also known as non-synonymous SNPs (nsSNPs). The primary goal is to elucidate the mechanisms through which functional SAPs exert their effects, and ultimately interrogating this information for association with complex phenotypes. This work focuses on coagulation factors involved in the coagulation cascade pathway which plays a vital role in the maintenance of homeostasis in the human system. We developed an integrated coagulation variation database, CoagVDb, which makes use of the biological information from various public databases such as NCBI, OMIM, UniProt, PDB and SAPs (rsIDs/variant). CoagVDb enriched with computational prediction scores classify SAPs as either deleterious or tolerated. Also, various other properties are incorporated such as amino acid composition, secondary structure elements, solvent accessibility, ordered/disordered regions, conservation, and the presence of disulfide bonds. This specialized database provides integration of various prediction scores from different computational methods along with gene, protein, and disease information. We hope our database will act as a useful reference resource for hematologists to reveal protein structure-function relationship and disease genotype-phenotype correlation.
author	Ali,Shabana Kouser George Priya Doss,C Thirumal Kumar,D Zhu,Hailong
author_facet	Ali,Shabana Kouser George Priya Doss,C Thirumal Kumar,D Zhu,Hailong
author_sort	Ali,Shabana Kouser
title	CoagVDb: a comprehensive database for coagulation factors and their associated SAPs
title_short	CoagVDb: a comprehensive database for coagulation factors and their associated SAPs
title_full	CoagVDb: a comprehensive database for coagulation factors and their associated SAPs
title_fullStr	CoagVDb: a comprehensive database for coagulation factors and their associated SAPs
title_full_unstemmed	CoagVDb: a comprehensive database for coagulation factors and their associated SAPs
title_sort	coagvdb: a comprehensive database for coagulation factors and their associated saps
publisher	Sociedad de Biología de Chile
publishDate	2015
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602015000100035
work_keys_str_mv	AT alishabanakouser coagvdbacomprehensivedatabaseforcoagulationfactorsandtheirassociatedsaps AT georgepriyadossc coagvdbacomprehensivedatabaseforcoagulationfactorsandtheirassociatedsaps AT thirumalkumard coagvdbacomprehensivedatabaseforcoagulationfactorsandtheirassociatedsaps AT zhuhailong coagvdbacomprehensivedatabaseforcoagulationfactorsandtheirassociatedsaps
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CoagVDb: a comprehensive database for coagulation factors and their associated SAPs

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