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A Large-Scale Comparison of Computational Models on the Residue Flexibility for NMR-derived Proteins

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As an alternative to X-ray crystallography, nuclear magnetic resonance (NMR) has also emerged as the method of choice for studying both protein structure and dynamics in solution. However, little work using computational models such as Gaussian network model (GNM) and machine learning approaches has focused on NMR-derived proteins to predict the residue flexibility, which is represented by the root mean square deviation (RMSD) with respect to the average structure. We provide a large-scale comparison of computational models, including GNM, parameter-free GNM and several linear regression models using local solvent exposures as inputs, based on a dataset of 1609 protein chains whose structures were resolved by NMR. The result again confirmed that the correlation of GNM outputs with raw RMSD values was better than that using B-factors of X-ray data. Nevertheless, it was also concluded that the parameter-free GNM and the solvent exposure based linear regression models performed worse than GNM when predicting RMSD, contrary to results using X-ray data. The discrepancy of residue flexibility prediction between NMR and X-ray data is likely attributable to a combination of their physical and methodological differences.

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Keywords: Debye-Waller temperature factor; Gaussian network model; Residue flexibility; Vermont Company; crystallographic structures; linear regression model; microtubules; molecular dynamic simulation; root mean square deviation; thermal stability

Document Type: Research Article

Publication date: February 1, 2012

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.
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