Similar protocols

Pipeline publication

[…] otocol defined a cubic box upon the edge approximately 1.2 nm from the protein complexes periphery and creates a neutral system using 0.145 M NaCl model. A maximum of 5,000 steps of steepest descents [] minimization was employed to remove bad van der Waals contacts. In equilibration section, a position-restrained molecular dynamics with the linear constraint algorithm for all bonds was performed using NVT equilibration, Berendsen weak thermal coupling method, and Particle Mesh Ewald method. A total of 10 ns production simulations were performed with time step in unit of 2 fs under NPT ensembles and Particle Mesh Ewald (PME) option. The 10 ns MD trajectories were then analyzed by a series of Gromacs protocols, and the presumable pathways for small molecule under dynamic conditions were analyzed by the CAVER 3.0 program []., The disordered disposition of TRAF6 protein was predicted by PONDR-Fit protocol [] with the sequence from Swiss-Prot (UniProtKB: Q9Y4K3). The result displayed in indicates that the key residues in the binding domain do not lie in disordered disposition and they can form a stable binding domain in protein folding. As the residues in the binding domain have no significant variation, the crystallography structure of TRAF6 protein is a suitable receptor for docking simulation., After virtual screening, the chemical scaffold top TCM compounds ranked by Dock Score [] are shown in with the scoring function of -PLP1, -PLP2, and -PMF. For the top three TCM compounds, tryptophan, diiodotyrosine, and saussureamine C, which were extracted from Saussurea lappa C […]

Pipeline specifications

Software tools GROMACS, CAVER, PONDR-FIT