Biomedical subjects

Peter Revesz

Publications and source records attributed to Peter Revesz.

3 recordsLinked to original sources

PubMed2006

FAST-NMR: functional annotation screening technology using NMR spectroscopy.

An abundance of protein structures emerging from structural genomics and the Protein Structure Initiative (PSI) are not amenable to ready functional assignment because of a lack of sequence and structural homology to proteins of known function. We describe a high-throughput NMR methodology (FAST-NMR) to annotate the biological function of novel proteins through the structural and sequence analysis of protein-ligand interactions. This is based on basic tenets of biochemistry where proteins with similar functions will have similar active sites and exhibit similar ligand binding interactions, despite global differences in sequence and structure. Protein-ligand interactions are determined through a tiered NMR screen using a library composed of compounds with known biological activity. A rapid co-structure is determined by combining the experimental identification of the ligand binding site from NMR chemical shift perturbations with the protein-ligand docking program AutoDock. Our CPASS (Comparison of Protein Active Site Structures) software and database are then used to compare this active site with proteins of known function. The methodology is demonstrated using unannotated protein SAV1430 from Staphylococcus aureus.

Amino Acid Sequence↗

PubMed2006

Comparison of protein active site structures for functional annotation of proteins and drug design.

Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary-sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein's activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand-binding sites to infer biological function and aid in drug discovery. The CPASS database comprises the ligand-defined active sites identified in the protein data bank, where the CPASS program compares these ligand-defined active sites to determine sequence and structural similarity without maintaining sequence connectivity. CPASS will compare any set of ligand-defined protein active sites, irrespective of the identity of the bound ligand.

Adenosine Triphosphate↗

PubMed2006

Spatiotemporal reasoning about epidemiological data.

OBJECTIVE: In this article, we propose new methods to visualize and reason about spatiotemporal epidemiological data. BACKGROUND: Efficient computerized reasoning about epidemics is important to public health and national security, but it is a difficult task because epidemiological data are usually spatiotemporal, recursive, and fast changing hence hard to handle in traditional relational databases and geographic information systems. METHODOLOGY: We describe the general methods of how to (1) store epidemiological data in constraint databases, (2) handle recursive epidemiological definitions, and (3) efficiently reason about epidemiological data based on recursive and non-recursive Structured Query Language (SQL) queries. RESULTS: We implement a particular epidemiological system called West Nile Virus Information System (WeNiVIS) that enables the visual tracking of and reasoning about the spread of the West Nile Virus (WNV) epidemic in Pennsylvania. In the system, users can do many interesting reasonings based on the spatiotemporal dataset and the recursively defined risk evaluation function through the SQL query interfaces. CONCLUSIONS: In this article, the WeNiVIS system is used to visualize and reason about the spread of West Nile Virus in Pennsylvania as a sample application. Beside this particular case, the general methodology used in the implementation of the system is also appropriate for many other applications. Our general solution for reasoning about epidemics and related spatiotemporal phenomena enables one to solve many problems similar to WNV without much modification.

Animals↗