Saturday, August 15, 2015

New preprint: ProCS15: A DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

2015.08.24 Update: the paper has now been submitted to PeerJ

Here is a new manuscript that just appeared on PeerJ Preprints today.  I plan to submit the paper in a week or so and am very interested in feedback.  There are several ways of providing feedback: here, comments below, on PeerJ, on Authorea (where I wrote the paper), and on PubPeer (which allows for anonymous comments).

I am thinking of submitting it to PeerJ but other ideas are also welcome.

Here's the abstract
We present ProCS15: A program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7 - 1.1, 0.2 - 0.4, and 1.8 - 2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.

This work is licensed under a Creative Commons Attribution 4.0

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