Journal of Computational Chemistry

The one-step perturbation method was applied to tackle a challenging computational problem, that is, the calculation of the folding free enthalpies of six hepta-β-peptides with different, nonpolar, and polar, side chains at the fifth residue. Different reference states were designed to better sample the conformational space of the peptides. For the peptides with polar side chains, post simulation rotational sampling of the side chain torsional angles was carried out.

The interaction of ureido-benzenesulfonamides inhibitor with human carbonic anhydrase enzyme including binding parameters, inhibition constant, thermodynamic parameters, and active site metal-ligand bonding nature have been systematically studied by QM/MM simulation, molecular docking, and NBO analysis. Molecular docking predicts the best dock pose compared to X-ray crystallographic structure within RMSD range (<1.50Å). These findings can be extended to other carbonic anhydrase isoforms with the possibility of designing new inhibitors.

We present a novel method of constructing protein backbones from C_α coordinates which we have implemented in a program named PD2 ca2main. Our method uses Gaussian mixture models to model short peptide fragments and build a library of "letters" which make up a structural alphabet. Given a series of C_α, the best fitting letters can then be used to insert missing backbone atoms. PD2 ca2main is available as C++ source code and a webserver.

The calculation of the electronic structure of large systems is facilitated by expanding the two-center distributions in terms of one-center functions. The partition–expansion method is an alternative to the standard projection methods which yields a systematic procedure for improving the fit of two-center distributions in pairs of one-center expansions. The method does not require auxiliary basis sets for projection and it allows to attain accurate expansions at a reduced cost.

The structural characterization of the major histocompatibility complex a-helices in reaction to different loaded peptides and liganded T cell receptors is an essential step in understanding how very early T cell activation takes place. For this purpose, we introduce a new differential geometric methodology to characterize these helices in a structured and comparable way.