Collaborative Projects
Our collaborative projects focus on the analysis of protein-protein interactions (3 projects) and a variety of collaborations related to method development and applications of drug discovery, including protein drugs.
Optimization and Learning Strategies for Protein Docking
Pirooz Vakili, Ioannis Paschalidis, Dima Kozakov, and Sandor Vajda Supported by: NIH R01 GM135930 “Optimization and Learning Strategies for Protein Docking” (PI: Pirooz Vakili) NIH R35 GM118078 “Analysis and Prediction of Molecular Interactions” (PI: Sandor Vajda) NSF DBI 1759472 “Collaborative Research: ABI Development: The next stage in protein‐protein docking” (PI: Sandor Vajda) NIH R21 GM127952... More
Improving the ClusPro Protein-Protein Docking Server
Sandor Vajda, Dima Kozakov, Ioannis Paschalidis, and Pirooz Vakili Supported by: NIH R35 GM118078 “Analysis and Prediction of Molecular Interactions” (PI: Sandor Vajda) NSF DBI 1458509 “ABI Development: Utilization of diverse data in exploring protein‐protein interactions” (PI: Sandor Vajda) NSF DBI 1759472 “Collaborative Research: ABI Development: The next stage in protein‐protein docking” (PI: Sandor... More
Stochastic Dynamic Modeling of Cellular Protein Interactions
Mark Kon, Julio Castrillon, Dmitri Beglov, and Sandor Vajda Supported by: NIH R01GM131409 “Stochastic Dynamic Modeling of Cellular Protein Interactions” (PI: Mark Kon) NIH R35 GM118078 “Analysis and Prediction of Molecular Interactions” (PI: Sandor Vajda) Stochastic methods for modeling molecular-protein interactions form an entirely new set of ap-proaches to the important biological goal of... More
Analysis of Protein-Metabolite Interactions
Sandor Vajda, Andrew Emili, and Daniel Segre Supported by: Supplement to NIH R35 GM118078 “Analysis and Prediction of Molecular Interactions” (PI: Sandor Vajda) for the purchase of a Mass Spectrometer. The Emili lab performs mass spectrometry pull-down experiments to provide information on small molecules that bind specific cellular proteins. The data provided... More
Antibody Modeling and Epitope Prediction
Dmitri Beglov, Sandor Vajda, and Dima Kozakov Supported by: NIH R43 GM134769 Software For Antibody Epitope Prediction (PI: Dmitri Beglov) Accurate epitope prediction is important for the development of antibody-based therapies. When multiple new antibodies are discovered against the whole antigen, their epitopes and, therefore, potential novelty and mechanism of action are usually... More
Development and applications of fragment based drug design methods
Sandor Vajda, Karen Allen, George Keseru, and Adrian Whitty Supported by: NIH R35 GM118078 “Computational Mapping of Proteins for the Binding of Ligands” (PI: Vajda) Fragment-based drug design (FBDD) is a combinatorial approach in which individual fragments binding to regions of the target site are selected from a fragment library, and... More
Inhibitors targeting protein-protein interactions
Adrian Whitty, Karen Allen, John Porco, and Sandor Vajda. Supported by: NIH R01 GM117350 “Molecular Mechanism Of The Nfkappab Essential Modulator (Nemo) Scaffold Protein Mutated In Human Immunodeficiencies” (PI: Adrian Whitty) NIH R35 GM118078 “Analysis and Prediction of Molecular Interactions” (PI: Sandor Vajda) NF-κB essential modulator (NEMO) is a component of the Inhibitor... More
Development of Mathematical and Computational Methods for Improved Protein-Protein Docking
Vajda, Kozakov, Paschalidis, and Vakili groups Supported by: NIH R01 GM061867 “A multistage approach to protein-protein docking” (PI: Vajda) NIH R01 GM093147 “Refinement Methods for Protein Docking based on Exploring Multi-Dimensional Energy Funnels” (PI: Paschalidis and Kozakov) NSF DBI 1147082 “ABI Development: Refinement Algorithms and Server for Protein Docking” (PI: Vajda... More
Computational selection of small molecule inhibitors of the eIF4E:eIF4G protein-protein complex involved in cancer
Vajda and Beglov groups Supported by: American Cancer Society institutional pilot grant IRG 72 001-36-IRG (PI: D. Beglov) The objective of this project is to identify novel inhibitors of the translation initiation factor eIF4E by extensive, fast and reliable screening of large virtual libraries of chemical compounds. EIF4E is a well validated drug target which is misused by... More
GPU Accelerated Protein Docking Software with Flexible Refinement
Herbordt, Vajda, and Kozakov groups, Acpharis Inc (Faculty startup by Vajda) Supported by: NIH R41GM101907-01 “GPU Accelerated Protein Docking Software with Flexible Refinement” (PI: Herbordt) Based on the results of CAPRI (Critical Assessment of Predicted Interactions), a worldwide protein docking competition, PIPER, developed in the Vajda lab, is among the best protein-protein... More