Project 10470 and T4 Lysozyme
(Guest post by Kyle Beauchamp from the Chodera lab.) In the Chodera lab, we’d like to understand how drugs bind to proteins, particularly for challenging diseases such as cancer or…
Read moreNews
Activation pathway of Src kinase reveals intermediate states as targets for drug design.
D. Shukla, Y. L. Meng, B. Roux, and V. S. Pande. Nat Commun 5 (2014) Unregulated activation of Src kinases leads to aberrant signalling, uncontrolled growth and differentiation of cancerous…
Read moreStatistical model selection for Markov models of biomolecular dynamics.
R. T. McGibbon, C. R. Schwantes, and V. S. Pande. J Phys Chem B. 118 6475-81 (2014) Markov state models provide a powerful framework for the analysis of biomolecular conformation…
Read moreDynamical Phase Transitions Reveal Amyloid-like States on Protein Folding Landscapes.
J. K. Weber, R. L. Jack, C. R. Schwantes, and V. S. Pande. Biophys J. 107(4) 974-82 (2014). Developing an understanding of protein misfolding processes presents a crucial challenge for…
Read moreDescribing protein folding via temperature-jump two-dimensional infrared spectroscopy and Markov state models.
C. R. Baiz, Y.-S. Lin, C. S. Peng, K. A. Beauchamp, V. A. Voelz, V. S. Pande, and A. Tokmakoff. Biophysical Journal, 106 1359-1370 (2014) The folding mechanism of the…
Read moreCloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways.
K. J. Kohlhoff*, D. Shukla*, M. Lawrenz*, G. R. Bowman, D. E. Konerding, D. Belov, R, B. Altman, and V. S. Pande.  Nature Chemistry 6 15-21 (2014) We applied methods developed and honed…
Read moreNew projects to help design selective inhibitors of protein methyltransferases
The Chodera lab has teamed up with Luo lab at MSKCC to study another important class of cancer targets: protein methyltransferases. These are protein-modifying enzymes that catalyze the transfer of…
Read moreInvestigating conformations accessible by Abl kinase- drug target for chronic myelogenous leukemia
Guest post by Sonya Hanson, postdoc in the Chodera lab. (Project 10472) We’re working our way through the kinase family here at the Chodera lab. You may have seen Danny’s…
Read moreA new project to study early folding events in apomyoglobin
In a new NSF-funded collaboration, the Voelz Lab is working with the Roder Lab at Fox Chase Cancer Center to study early folding events in apomyoglobin. Apomyoglobin (myoglobin without the…
Read moreCombining simulation and experiments to solve molecular structures
The Voelz lab has been making progress on combining simulation and experiments to solve molecular structures. Most molecules do not have a single rigid structure in solvent. Instead, they exist…
Read more