Sensitivity of Binding Free Energy Calculations to Initial Protein Crystal Structure

Towards accurate free energy calculations in ligand protein-binding studies.

Cells contain a multitude of different chemical reaction paths running simultaneously and quite independently next to each other. This amazing feat is enabled by molecular recognition, the ability of biomolecules to form stable and specific complexes with each other and with their substrates. A better understanding of this process, i.e. of the kinetics, structures and thermodynamic properties o...

Carbohydrate-protein interactions: structure, dynamics and free energy calculations

The current thesis presents work on the structure and dynamics of oligosaccharides and polysaccharides as well as the free energetics of carbohydrate-protein interactions. By applying various computational tools such as molecular dynamics simulations, our in-house fast sugar structure prediction software, replica exchange molecular dynamics, homology modeling, umbrella sampling, steered molecul...

How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conforma...

Free energy calculations and ligand binding.

From Structure to Function with Binding Free Energy Calculations for Codon Reading, Riboswitches and Lectins

Sund, J. 2013. From Structure to Function with Binding Free Energy Calculations for Codon Reading, Riboswitches and Lectins. Acta Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1072. 58 pp. Uppsala. ISBN 978-91-554-8750-8. Molecular association is part of many important processes in living cells. Computational metho...