Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in ...
Guo. Part of the structural computation and molecular dynamics simulation was performed on the High-performance Computing Platform of Peking University and the Computing Platform of the Center for Life Science, Peking University. The work is supported by grants from the Ministry of Science and ...
Molecular dynamics simulation Molecular dynamic simulations were performed by Gromacs 2018.5. The receptor was prepared and capped by the Protein Preparation Wizard (Schrodinger 2017-4), while the titratable residues were left in their dominant state at pH 7.0. The complexes were embedded in a bilayer...
In this study, we generated three-dimensional models of five RNA aptamers from their sequence using mFold, RNAComposer web server, and molecular dynamics simulation. The model structures were then evaluated and compared with the experimentally determined structures. This study show...
webserver. The clash-score ranged from 0.65 for the alpha variant to 2.62 for the delta. That value is well within the 98th percentile, based on analysis of 1,784 crystal structures. The Molprobity score ranged from 1.34 for the alpha variant to 1.9 for C.36. The latter value is ...
Domain-localized linear interpolation of the atoms from a molecular dynamics simulation performed with MODELLER in ePMV and a hinged bone skeleton (host) for large domain motion was used to morph between the two experimental conformations, host-based vibration was applied to the ligand to imply ...
Pyruvate Kinase M2 (PKM2) isozyme is categorized under the pyruvate kinase family, and it catalyzes the final step in the glycolysis process. PKM2 enzyme is highly expressed in tissues with anabolic functions like embryonic cells and cancer cells. Experimentalists have identified PKM2 as an arsenic ...
Figure 10 shows the molecular dynamics of Lymecycline and fucosterol with GRB2 protein ligand complex and GRB2 protein (RMSD, RMSF and hydrogen bond analysis). For RMSD (Fig. 10A), in the 100 ns simulation, all the three systems reached the equilibrium state quickly. In the end, the RMSD...
Since the structures, especially main chain conformations, of two EF-lobes in holo-form are quite similar; this is a good example to evaluate the effect of side chains for structural dynamics. We analyzed the structure of calmodulin using molecular dynamics and found differences in conformational ...
Bioinformation ESBRI: a web server for evaluating salt bridges in proteins Bioinformation., 3 (2008), pp. 137-138, 10.6026/97320630003137 View in ScopusGoogle Scholar [47] M. Pasenkiewicz-Gierula, K. Murzyn, T. Róg, C. Czaplewski Molecular dynamics simulation studies of lipid bilayer system...