Dmytro Kozakov
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 […]
Refinement Methods for Protein Docking based on Exploring Multi-Dimensional Energ
All successful state-of-the-art protein docking methods employ a so called multistage approach. At the first stage of such approaches a rough energy potential is used to score billions of conformations. At a second stage, thousands of conformations with the best scores are retained and clustered based on a certain similarity metric. Cluster centers correspond to […]