We use computational and theoretical methods to study the structure and function of proteins, nucleic acids and membranes. A current focus involves the combined use of physical and chemical methods, amino acid sequence analysis, three dimensional structure analysis and data mining as tools in bioinformatics and genome analysis. Specific research areas include: The development of accurate computational methods to predict protein structure from amino acid sequence; the use of three-dimensional structural information to identify relationships between remote sequence homologs and the use of these relationships in the analysis of genomic information; the study of the physical chemical principles that underlie protein and RNA folding, protein-protein, protein-nucleic acid and protein-membrane interactions; the development of computational methods to identify protein function based on protein structure; the application of computational tools to the understanding of problems of biological importance such as subcellular localization in protein/membrane systems and the specificity of protein-protein interactions in signaling pathways.
As part of our research program we make a significant effort in software development. The programs we have developed include: DelPhi, which calculates the electrostatic properties of biological macromolecules; GRASP, which maps electrostatic and other properties on macromolecular surfaces; GRASS, which is a web-based GRASP server; SPIN; a server to describe interfaces formed by Macromolecules; PrISM (Protein Informatics System for Modeling). PrISM is an interactive program that analyzes protein sequences and structures and contains novel threading and homology modeling techniques.
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Selected Publications
Honig, B. (1999) Protein Folding: From the Levinthal Paradox to Structure Prediction. J. Mol. Biol. 293:283-293.Sheinerman, F., Norel, R. and Honig, B. (2000) Electrostatic Aspects of Protein-protein Interactions. Curr. Opinion in Struc. Biol. 10:153-159.
Petrey, D. and Honig, B. (2000) Free Energy Determinants of Tertiary Structure and the Evaluation of Protein Models. Protein Science 9:2181-2191.
Yang, A.-S. and Honig, B. (2000) An Integrated Approach to the Analysis of Sequence and Structure. I. Protein Structural Alignment and a Quantitative Measure for Protein Structural Distance. J. Mol. Biol. 301: 665-678.
Xiang, Z. and Honig, B. (2001) Extending the Accuracy Limits of Prediction for Side Chain Conformations. J. Mol. Biol. 311:421-430.
Norel, R., Sheinerman, F., Petrey, D. and Honig, B. (2001) Electrostatics Contributions to Protein-Protein Interactions: Fast Energetic Filters for Docking and Their Physical Basis. Prot. Sci. 10:2147-2161.