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R. Matthew Ward Baylor College of Medicine Department: SCBMB Program Address: Department of Molecular and Human Genetics Lichtarge Lab One Baylor Plaza Houston, TX 77030 Phone: (713) 798-5197 Fax: (713) 798-6325 Email: robert.ward@bcm.tmc.edu Web: http://mammoth.bcm.tmc.edu/

Education

B.A. University Scholars, Bioinformatics Emphasis, Baylor University (2003)
Mentor: Olivier Lichtarge, M.D., Ph.D.

Honors

W. M. Keck Predoctoral Fellow

Research Topic

Interpreation and application of evolutionary trace results within the context of primary structure

Research Description

Computational identification of functional sites in proteins can aid in-depth studies of protein function, drug targeting, and protein engineering, saving expensive and time-consuming experimental work. The evolutionary trace (ET) is one such technique for identifying residues that are likely to have crucial functional or structural roles. These residues display significant clustering in the tertiary structure of proteins to form functional sites. The extent of this clustering provides a measure of the quality of the trace analysis.

In its current form, ET requires a three-dimensional structure in order to perform this analysis. An examination of evolutionary traces of a set of proteins from the PDB shows significant clustering of important residues in the primary structure of the proteins. Like three-dimensional clustering, one-dimensional clustering in the primary structure of the protein can be used to formally assess the quality of ET analysis when a structure is not available. This evidence supports extending ET to genes currently beyond its reach, such as proteins without solved structures or possibly even non-protein coding nucleic acids.

Additionally, I am interested in applying ET to make predictions about the effects of non-synonymouse single nucleotide polymorphisms (nsSNPs) using machine learning algorithms, and in using ET to build 3D templates and search for functional homologs to perform functional annotation.

Selected Publications

• Kristensen, D.M., B. Chen, V. Fofanov, R.M. Ward, A.M. Lisewski, M. Kimmel, L. Kavraki, and O. Lichtarge (2006). "Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity." Protein Science: In Press.

Last edited on: January 06, 2006