Sandor Vajda
Optimizing and Learning Strategies for Protein Docking
Protein docking is defined as predicting the three-dimensional structure of the docked complex based on knowledge of the structure of the components. Experimental techniques for this purpose are often expensive, time-consuming, and in some cases, not feasible; hence the need for computational docking methods. The problem of finding the docked conformation is generally formulated as […]
Collaborative Research: ABI Development: The next stage in protein-protein docking
Protein-protein interactions are integral to many mechanisms of cellular control, including protein localization, allosteric and gene regulation and signal transduction, and therefore their characterization is an important task for both experimental and computational approaches to systems biology. Genome-wide proteomics studies provide a growing list of putative protein-protein interactions, and demonstrate that most if not all […]
Analysis and Prediction of Molecular Interactions
The research in our lab focuses on molecular recognition using computational methods and follow-up validation experiments. Our primary target areas are (1) protein-protein docking and (2) exploring binding properties of proteins by computational solvent mapping. Protein docking methods are needed because many important interactions occur in weak, transient complexes that are not amenable to direct […]
AF: Small: Manifold optimization algorithms for protein-protein docking
Proteins are the major building blocks of the cell. Many proteins perform their function by interacting with other proteins. In a typical cell hundreds of thousands of different protein interactions take place. Characterizing these interactions helps elucidate how living organisms function at the molecular level, contributes towards the development of treatments against diseases such as […]
ABI Development: Utilization of Diverse Data in Exploring Protein-Protein Interactions
Each living cell is packed with proteins that continuously interact with each other in response to envirtonmental and other signals to control the cell’s growth and eventual fate. The analysis of such interactions is crucial for understanding signal transduction pathways that drive cell differentian during development and throughout the life an an organism. These pathways […]
ABI Development: Refinement Algorithms and Server for Protein Docking
Protein-protein interactions are integral to virtually all biological pathways. Predicting these interactions and the function of the protein complex in key to understanding how biological pathways function. Detailed multistage docking algorithms, which starts from the unbound structures of two proteins, can determine the structure of the protein complex. The docking server, ClusPro, strives to make […]
Computational mapping of proteins for the binding of ligands
The proposal requests the renewal of the grant “Computational Mapping of Proteins for the Binding of Ligands”. Mapping globally samples the surface of target proteins using fragment sized molecular probes. The general goals of mapping are determining binding hot spots, i.e., regions of proteins that are major contributors to the binding free energy, and identifying […]