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

Shabana Kouser Ali, C. George Priya Doss*, D. Thirumal Kumar, Hailong ZHU

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

4 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number35
JournalBiological Research
Volume48
DOIs
Publication statusPublished - 2015

Scopus Subject Areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

User-Defined Keywords

  • Align GVGD
  • Coagulation cascade pathway
  • Coagulation factor proteins
  • Fathmm
  • I-Mutant 3
  • PhD-SNP
  • PolyPhen 2
  • SIFT
  • Single amino acid substitutions
  • SNAP
  • SNPs&GO

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