David Bednar

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.

TL;DR: A new module for the estimation of thermodynamic stabilities using the Rosetta and FoldX suites has been introduced which prevents destabilizing mutations among pre-selected variants entering experimental testing.

TL;DR: CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures that provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics.

TL;DR: FireProt is a robust computational strategy for predicting highly stable multiple-point mutants that combines energy- and evolution-based approaches with smart filtering to identify additive stabilizing mutations and can be applied to any protein for which a tertiary structure and homologous sequences are available.

TL;DR: Caver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels, and study of the ligands’ transport through these transport pathways, the first interactive tool allowing both the analyses within a single graphical user interface.