Neighborhood Preference of Amino Acids in Protein Structures and its Applications in Protein Structure Assessment.

Scientific Reports
Siyuan LiuHaiguang Liu

Abstract

Amino acids form protein 3D structures in unique manners such that the folded structure is stable and functional under physiological conditions. Non-specific and non-covalent interactions between amino acids exhibit neighborhood preferences. Based on structural information from the protein data bank, a statistical energy function was derived to quantify amino acid neighborhood preferences. The neighborhood of one amino acid is defined by its contacting residues, and the energy function is determined by the neighboring residue types and relative positions. The neighborhood preference of amino acids was exploited to facilitate structural quality assessment, which was implemented in the neighborhood preference program NEPRE. The source codes are available via https://github.com/LiuLab-CSRC/NePre.

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Citations

Jun 27, 2020·Scientific Reports·Xiang GaoHaiguang Liu

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Methods Mentioned

BETA
X-ray
electron microscopy
PISA

Software Mentioned

R
3DRobot
DFIRE
RW
BLAST
- TASSER
Modeller
Tasser
F I
Rosetta

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