Combining MD simulation with wet-lab experiments has become an indispensable complement in the investigation of several important and intricate biological processes. Various tools like principal component analysis, cross-correlation analysis, and residues interaction network analysis are additional useful ...
Computer SimulationComputational BiologyHydrogen BondingMolecular dynamics (MD) simulations and nuclear magnetic resonance spin-relaxation measurements provide detailed insights into ps-ns structural dynamics of proteins. An analysis of discrepancies between the two methods is presented for the B3 immunoglobulin...
To evaluate how well the protein structure is preserved in the simulation, we computed the mean squared deviation (MSD) using the final 1 μs of simulation (Fig.2a). For both ff14SB and C36m, the structure is well-preserved overall, with the loop regions and C-terminal tail exhibiting t...
Thus, when the ratio of protein and detergents is unknown, to find an optimal MD simulation system, one can build multiple protein–micelle systems with detergent numbers exceeding the micelle aggregation number. The KvAP VSD simulation system was chosen to test this idea and produced results ...
Molecular dynamics (MD) calculations were executed for a system consisting of a protein, such as a receptor or ligand, benzene molecules initially placed near hydrophobic amino acid residues, and water molecules, in order to form clusters of benzene molecules. Approximate fittings between the BCs ...
About this protocol Cite this protocol Kumar, V., Yaduvanshi, S. (2023). Protein-Protein Interaction Studies Using Molecular Dynamics Simulation. In: Sousa, Â., Passarinha, L. (eds) Advanced Methods in Structural Biology. Methods in Molecular Biology, vol 2652. Humana, New York, NY. http...
(Pearsonr = 0.66/0.70 for ff14SB/C36m). Both force fields accurately describe the increased mobility of the loop regions compared to the rest of the protein. Previous MD simulation studies of protein crystals reported similarly high correlations of computed and experimental B-factors25,26....
(transparent gray isosurfaces) are shown. The two binding pathways observed are depicted as blue and green arrows. The histogram of the RMSD of dasatinib and the contact protein beads is depicted on the lower right.cSimulation box containing the AAK1 and one molecule of baricitinib (red) ...
many processes require coordination and hence communication which quickly becomes a bottleneck. This is exacerbated with more powerful hardware as internal node communication for a single simulation on a single GPU can also become a bottleneck. This problem has been addressed for CPU parrallelism with...
However, MD simulation starting from the unbound porcine pancreatic elastase alone shows a conformational switch leading to the recovery of the interaction interface with elafin with a cluster center ROC AUC of 0.92 and perfect recovery rate of predicted binding interface (i.e., 3 residues in this...