Collaborative Projects

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

Development of fragment based drug design methods using computational, X-ray crystallography, and NMR approaches

Vajda, Kozakov, Allen, and Whitty groups Supported by: NIH R01 GM064700 “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 then combined to form... More

Analysis of ligand binding to DNA and RNA molecules

Vajda, Kozakov, and Frank-Kamenetskii groups Small molecules that bind to DNA are extremely useful as biochemical tools for the visualization of DNA both in vitro and inside the cell. Additionally, the clinical significance of DNA-binding compounds can hardly be overstated, as many anticancer regimens include a compound that binds to and/or... More

Inhibitors targeting protein-protein interactions: Applications to NEMO

Whitty, Allen, Porco, Vajda, and Kozakov groups Supported by: NIH R01 GM094551 “Design of macrocyclic inhibitors of the NEMO/IKKα/β protein-protein interaction” (PI: Whitty) NIH R01 GM064700 “Computational Mapping of Proteins for the Binding of Ligands” (PI: Vajda) NF-κB essential modulator (NEMO) is a component of the Inhibitor of κB (I-κB) kinase (IKK) complex, More

Targeting protein translation initiation for cancer therapy

Vajda, Porco, Kozakov, and Beglov groups, in collaboration with Jerry Pelletier (McGill University, Montreal) Supported by: NIH R01 GM064700 “Computational Mapping of Proteins for the Binding of Ligands” (PI: Vajda) Protein synthesis presents an emerging class of cancer drug targets. The translation process occurs in three phases: initiation, elongation, and termination, with initiation... More

The molecular origin of receptor-based developmental and reproductive toxicity

Vajda and Beglov groups, in collaboration with the Boston University Superfund Research Project Supported by: NIEHS P42ES007381 Receptor-Based Developmental And Reproductive Toxicity Of Superfund Chemicals (PI: D. Ozonoff) The Biomolecular Engineering Research Center is part of the Bioinformatics and Molecular Modeling Research Support Core, which offers computational tools, expertise, and services to a... More