Document Type

Article

Publication Date

2011

DOI

10.1371/journal.pone.0019238

Publication Title

PLOS One

Volume

6

Issue

4 (e19238)

Pages

1-14

Abstract

The criterion to determine residue contact is a fundamental problem in deriving knowledge-based mean-force potential energy calculations for protein structures. A frequently used criterion is to require the side chain center-to-center distance or the C-alpha-to-C-alpha atom distance to be within a pre-determined cutoff distance. However, the spatially anisotropic nature of the side chain determines that it is challenging to identify the contact pairs. This study compares three side chain contact models: the Atom Distance criteria (ADC) model, the Isotropic Sphere Side chain (ISS) model and the Anisotropic Ellipsoid Side chain (AES) model using 424 high resolution protein structures in the Protein Data Bank. The results indicate that the ADC model is the most accurate and ISS is the worst. The AES model eliminates about 95% of the incorrectly counted contact-pairs in the ISS model. Algorithm analysis shows that AES model is the most computational intensive while ADC model has moderate computational cost. We derived a dataset of the mis-estimated contact pairs by AES model. The most misjudged pairs are Arg-Glu, Arg-Asp and Arg-Tyr. Such a dataset can be useful for developing the improved AES model by incorporating the pair-specific information for the cutoff distance.

Original Publication Citation

Sun, W.T., & He, J. (2011). From isotropic to anisotropic side chain representations: Comparison of three models for residue contact estimation. Plos One, 6(4), 1-14. doi: 10.1371/journal.pone.0019238

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