By applying REMD simulations we have performed comparative analysis of the conformational ensembles of amino-truncated Aβ10-40 peptide produced with five force fields, which combine four protein parameterizations (CHARMM36, CHARMM22*, CHARMM22/cmap, and OPLS-AA) and two water models (standard and modified TIP3P). Aβ10-40 conformations were analyzed by computing secondary structure, backbone flu...

The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a...

Long MD simulations (100 ns) for the important model cyclopentapeptide cyclo(D-Pro1-Ala2-Ala3-Ala4-Ala5) were performed in explicit DMSO solution using both OPLS-AA and AMBER03 force fields. Simulations revealed conformational transitions between two main conformers, a predominant one (population 93-99%) and a minor conformer (population 0.4-6.7%). These results are in excellent agreement with ...

similar procedure and the same type of interaction model were used for glucose solutions. Specifically, MD simulation was carried out using the DL_POLY2.0 package. The MD trajectories were generated using the SPC/E potential model for water and the optimized potential for liquid simulation (OPLS) all-atom force field for carbohydrates, developed by Jorgensen and co-workers, for both trehalose a...

We are honored to write the commentary for the inaugural report of “The Biology Behind. . . ” series in Clinical Cancer Research. We confess at the outset, however, that the reader conducting the most thorough survey of the cancer literature would not turn up any publications on BBI with either of our names in the author list (before now). Nevertheless, the scientific roots of “Clinical Modulat...

To compare the chemical differences between the medicinal and cultured oyster shells, their chemical profiles were investigated. Using the ultra performance liquid chromatography-electron spraying ionization-mass spectrometry (UPLC-ESI-MS), combined with principal component analysis (PCA) and orthogonal projection to latent structures discriminant analysis (OPLS-DA), the discrimination of the c...