title: CoagVDb: a comprehensive database for coagulation factors and their associated SAPs.
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.
authors.affiliation: Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India. shabanakouser@vit.ac.in.
authors.forename: Shabana Kouser
authors.initials: SK
authors.lastname: Ali
authors.affiliation: Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India. georgecp77@yahoo.co.in.|Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong. georgecp77@yahoo.co.in.
authors.forename: C George Priya
authors.initials: CG
authors.lastname: Doss
authors.affiliation: Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India. thirumalkumar.d@gmail.com.
authors.forename: D Thirumal
authors.initials: DT
authors.lastname: Kumar
authors.affiliation: Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong. hlzhu@comp.hkbu.edu.hk.
authors.forename: Hailong
authors.initials: H
authors.lastname: Zhu
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics*; D001779:Blood Coagulation Factors / Q000235:genetics*; D019295:Computational Biology; D016208:Databases, Factual; D005838:Genotype; D006801:Humans; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D020539:Sequence Analysis, Protein
chemical_list: D001779:Blood Coagulation Factors