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Peer-reviewedCC BY 4.0Scientific Reports

Quantifying side-chain conformational variations in protein structure.

  • Zhichao Miao
  • Yang Cao
Open at sourcePDFDOICite

Abstract

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

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Cite

BibTeXRIS
BibTeX
@article{miao2026quantifying,
  title = {{Quantifying side-chain conformational variations in protein structure.}},
  author = {Zhichao Miao and Yang Cao},
  journal = {Scientific Reports},
  year = {2026},
  month = sep,
  doi = {10.1038/srep37024},
  url = {https://univoak.hal.science/hal-05256671v1},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Quantifying side-chain conformational variations in protein structure.
AU  - Zhichao Miao
AU  - Yang Cao
PY  - 2026
DA  - 2026/09/10
JO  - Scientific Reports
DO  - 10.1038/srep37024
UR  - https://univoak.hal.science/hal-05256671v1
AB  - Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.
SN  - 2045-2322
ER  -