We derived analytical expressions for the error and efficiency of enhanced sampling methods such as parallel tempering and replica exchange using kinetic network models.
We developed a new implementation of the finite temperature string method coupled with Hamiltonian replica exchange to study coupled proton transfer steps in RNase H.
Recently, we developed a novel Markov chain-based analysis method, DHAM, for accurate calculation of kinetic rates in addition to free energies from biased or unbiased molecular simulations.
Phosphate processing enzymes are crucial to the majority of the biochemical processes that all living cells depend on, including signal transduction, gene regulation, metabolism and energy transfer.
However, it is not well understood how biological systems fine-tune the catalytic rates of phosphate transfer and hydrolysis reactions in order to achieve their precise function.
We are particularly interested in the context of forming various assemblies through protein-protein, protein-nucleic acid, or, importantly, protein-metal ion interactions using Mg.
We are involved in many exciting collaborations covering a wide range of research projects.
Our recent work on dUTPases is a long-standing collaboration with Beata Vertessy's group at the MTA, Budapest.
One of our main projects sheds light on RAF kinase activation mechanism in collaboration with Walter Kolch's group at UCD, Systems Biology Ireland.
We have several new collaborative projects with the group of Oren Scherman at Cambridge University.