Section: New Results

Flexible Docking of Protein-GAG Complexes

Modeling how flexible polymers bind to proteins presents enormous computational challenges due to the large conformational search space that arises from the many internal rotational degrees of freedom in polymer structures. In collaboration with Sergey Samsonov (Gdansk University, Poland), we extended our fragment-based flexible docking approach [83], [42] to model how flexible Glycosaminoglycans (GAGs) might bind to the surface of a known protein structure. A paper has been submitted to the Journal of Computational Chemistry.

In collaboration with Sjoerd de Vries (Univ Paris Diderot), we have created a new protein-glycan interaction force-field and integrated it in the ATTRACT docking engine [83]. We also participated in a comparative study of the main current protein-GAG docking methods.