Jiri Damborsky

TL;DR: A new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations is presented, and analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating.

TL;DR: This study constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated prediction tools, and returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools.

TL;DR: The strategies can be grouped into three main categories: isolation of novel enzymes functioning under extreme conditions, modification of enzyme structures to increase their resistance toward nonconventional media, and modification of the solvent environment to decrease its denaturing effect on enzymes.

TL;DR: Rhodococcus rhodochrous haloalkane dehalogenase mutants with up to 32-fold higher activity than wild type are obtained toward the toxic, recalcitrant anthropogenic compound 1,2,3-trichloropropane using a new strategy that identifies key residues in access tunnels connecting the buried active site with bulk solvent by rational design and randomized them by directed evolution.

TL;DR: This work studies the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites to propose novel integrated algorithms that allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations.