Archive

… 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)….

Taking into account the steps for the folding pathway of α-helical membrane proteins and relating biophysical parameters to each of these steps, we create a score capable of predicting the propensity for membrane localization and call it FP3mem. By creating a score (FP3mem) encompassing the biophysical parameters involved in the folding of α-helical transmembrane proteins, we provide a scale for […]

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

There are many methods to detect protein folding intermediates along MD-based protein folding/unfolding pathway. We study to define new computational metrics to find intermediates structures along in silico protein folding pathway.    

  • Note

    Holly Quran: "... If you are able to penetrate the provinces of heaven and earth, pass through them! but you shall not pass through except with a power!"

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