… We introduce a new method for predicting dissociation free energy of subunits by analyzing the structural and topological properties of a protein binding patch on a single subunit of the desired protein complex. The method needs the 3D structure of just one subunit and the information about the position of the intended binding site on the surface of that […]

… We study the interactions of OmpF with pentameric poly-nucleotides (poly-Ns) in silico. The poly-N molecule is forced to translocate through the lumen of OmpF. Subsequently, the structural and dynamical effects of translocation steps on protein and poly-N molecules are explored in detail…[full story at PCB]

…. Two specific endoplasmic reticulum calcium channels, ryanodine receptors (RyRs) and inositol 1,4,5-trisphosphate receptors (IP3Rs) play an important role in Ca2+ regulation. In the present study, we provided a 3D structure of RyR and IP3R by homology modeling, and we predicted their interactions with a known neuroprotective compound, 3-thiomethyl-5,6-(dimethoxyphenyl)-1,2,4-triazine (TDMT), as well as two inhibitors, dantrolene and 2-aminoethoxydiphenyl borate (2-APB)….

Here, we hope to develop valid coarse grained (CG) force filed to study protein aggregation.

Unraveling the basis of lethal and life treading diseases like cancers, neuro-degenerative diseases, AIDS, … are very hard without decoding the protein folding mysteries. Computational approaches pave the way for studying protein folding pathway in detail. Here, we hope to develop new approaches to facilitate the computational studies of protein folding.