Computational structural biology

Dynamics are essential for biomolecular function; conformational transformations and changes in mobility hold the key to understanding many biological interactions. Obtaining this type of information requires a dedicated experimental and/or computational effort, which is not feasible on a genomic scale. The main goal of the research by Prof. Dr. Wim Vranken is to improve or innovate:

  • The prediction from primary protein structure (sequence) of characteristics such as flexibility and conformation
  • The estimation of these characteristics directly from experimental information (bypassing the three dimensional structure level)
  • The three dimensional structure representation of proteins, so that it better reflects the experimental information

These goals can in turn lead to better interpretation and prediction of biological interactions.

The main approaches that drive this research are:

  • Statistical examination of the relation between experimental data and structure, so leading to new understanding of dynamical aspects
  • Improving the translation of experimental data to in silico coordinates to obtain a more accurate representation of protein structure and dynamics.

The experimental data currently mainly comes from Nuclear Magnetic Resonance (NMR), with the aim to capitalize on other biophysical techniques (SAXS, ITC, ...) in the future. The focus on proteins will be further extended to DNA, RNA and carbohydrates.

The current main projects are:

  • DynaMine, the first predictor of protein backbone dynamics from sequence only
    • Conservation and variation of backbone dynamics in evolution
    • Relation of backbone dynamics to functional sites and motifs
    • Extending the concept with side-chain dynamics and conformation (secondary structure propensity)
  • Effects of β-amino acids on the conformational space and stability of peptides.
  • Relation between chemical shift and protein structural changes

These projects are implemented in a joint data/software structure.

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