ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins
| Autor: | Lars Andersen Bratholm, Anders S. Christensen, Maher Channir, Jan H. Jensen, Anders S. Larsen |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Hydrogen
Computer science Biophysics chemistry.chemical_element lcsh:Medicine Tripeptide Bioinformatics Quantum chemistry General Biochemistry Genetics and Molecular Biology Protein structure General Neuroscience Chemical shift lcsh:R Computational Biology General Medicine Chemical shifts Nitrogen NMR Crystallography chemistry Yield (chemistry) General Agricultural and Biological Sciences Carbon |
| Zdroj: | PeerJ PeerJ, Vol 3, p e1344 (2015) Larsen, A S, Bratholm, L A, Christensen, A S, Channir, M & Jensen, J H 2015, ' ProCS15 : a DFT-based chemical shift predictor for backbone and C β atoms in proteins ', PeerJ, vol. 3, e1344 . https://doi.org/10.7717/peerj.1344 |
| ISSN: | 2167-8359 |
| DOI: | 10.7717/peerj.1344 |
| Popis: | We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβatoms 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. |
| Databáze: | OpenAIRE |
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