MulPSSM: a database of multiple position-specific scoring matrices of protein domain families

Abstract

Representation of multiple sequence alignments of protein families in terms of position-specific scoring matrices (PSSMs) is commonly used in the detection of remote homologues. A PSSM is generated with respect to one of the sequences involved in the multiple sequence alignment as a reference. We have shown recently that the use of multiple PSSMs corresponding to an alignment, with several sequences in the family used as reference, improves the sensitivity of the remote homology detection dramatically. MulPSSM contains PSSMs for a large number of sequence and structural families of protein domains with multiple PSSMs for every family. The approach involves use of a clustering algorithm to identify most distinct sequences corresponding to a family. With each one of the distinct sequences as reference, multiple PSSMs have been generated. The current release of MulPSSM contains ∼33 000 and ∼38 000 PSSMs corresponding to 7868 sequence and 2625 structural families. A RPS_BLAST interface allows sequence search against PSSMs of sequence or structural families or both. An analysis interface allows display and convenient navigation of alignments and domain hits. MulPSSM can be accessed at .

GraphProt: modeling binding preferences of RNA-binding proteins

“…The use of disjoint subgraphs gives a binding motif that is more expressive than the one offered by traditional position specific scoring matrices [37] because it takes the simultaneous interdependencies between sequence and structure information at different locations into account. Feature importance information can be used, not only to build accurate predictors, but can be subsequently processed to identify sequence and structure binding preferences.…”

Identification and Characterization of a Novel Deoxyhypusine Synthase in Leishmania donovani

“…Multiple alignment of amino acid sequences was performed using the program ClustalW (available on the World Wide Web) The bootstrap analysis was done and the phylogenetic tree was constructed using the software MEGA version 4.0 (27). DHSL20 and DHS34 protein sequences were searched against the multiple position-specific substitution matrix data base (MulPSSM) (28) of Pfam protein domain families (29) using an RPS-BLAST approach (30). Local alignments of DHS34 and DHSL20 protein were compared with human DHS to analyze the conservation of important amino acid residues.…”

Proteomics in India: the clinical aspect

“…NCBS has also come up with the DOQCS, which represents the collection of basic models of different signaling pathways [138–141]. Researchers at IISc, Bangalore have developed quite a few protein databases related to structure and function of protein kinases like ‘KinG’, NrichD, PALI, PRODOC and MulPSSM [142–144]. A number of protein databases such as PepBind, Immune Epitope Prediction Database & Tools, SEDB, Clostridium-DT(DB), and VPDB have originated from the Center of Bioinformatics in Pondicherry University [145–147].…”