We are interested in understanding proteins by means of theoretical methods. The research areas cover (but are not limited to):
o Sequence and structure classification; o Protein structure prediction; o Molecular evolution; o Construction and analysis of multiple sequence and structural alignments; o Analysis of genomic data; o Sequence-structure-function relationship in protein families.
The ultimate objective of protein computational biology is to classify available sequence-structure data into a biologically relevant, hierarchical system analogous to the one currently used in zoology and botany. Since sequence and structural similarities usually imply functional similarity, such classification is of indispensable value for biologists to aid in experimental design.
Our group combines sequence and structure analysis with evolutionary considerations to facilitate discoveries of biological significance. Two major directions are pursued: (i) development of new mathematical approaches for analysis of protein sequence-structure data; and (ii) implementation of available tools for solving biological problems by computer analysis.
RESEARCH INTERESTS
We study proteins by means of computational methods
RECENT PUBLICATIONS
Qi Y, Sadreyev RI, Wang Y, Kim BH, Grishin NV., "A comprehensive system for evaluation of remote sequence similarity detection" BMC Bioinformatics, 8(1):314, August 2007
Shi S, Zhong Y, Majumdar I, Sri Krishna S, Grishin NV., "Searching for three-dimensional secondary structural patterns in proteins with ProSMoS." Bioinformatics, 23(11):1331-1338, June 2007
Sadreyev RI, Tang M, Kim BH, Grishin NV., "COMPASS server for remote homology inference" Nucleic Acids Res, 35(Web Server issue):W653, May 2007
Pei J, Grishin NV., "MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information." Nucleic Acids Res, 34(16):4364-4374, August 2006
Cheek S, Krishna SS, Grishin NV., "Structural classification of small, disulfide-rich protein domains." J Mol Biol., 359(1):215-237, May 2006
SIGNIFICANT PUBLICATIONS
Grishin, N.V., "Fold change in evolution of protein structures." J. Struct. Biol., 134:167-185, 2001
Pei J, Grishin NV., "PROMALS: towards accurate multiple sequence alignments of distantly related proteins." Bioinformatics, 23(7):802-808, January 2007
Sadreyev R, Grishin NV, "COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance." J Mol Biol, 326(1):317-336, February 2003
Cheek S, Zhang H, Grishin NV., "Sequence and structure classification of kinases." J Mol Biol, 320(4):855-881, July 2002
Ginalski K, Rychlewski L, Baker D, Grishin NV., "Protein structure prediction for the male-specific region of the human Y chromosome." Proc Natl Acad Sci U S A, 101(8):2305-2310, February 2004
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