To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era.

ABSTRACT:

Motivation

Protein side-chain packing (PSCP), the problem of predicting side-chain conformation given a fixed backbone structure, has important implications in modeling of structures and interactions. However, despite the groundbreaking progress in protein structure prediction pioneered by AlphaFold, the existing PSCP methods still rely on experimental inputs, and do not leverage AlphaFold-predicted backbone coordinates to enable PSCP at scale.

Results

Here, we perform a large-scale benchmarking of the predictive performance of various PSCP methods on public datasets from multiple rounds of the Critical Assessment of Structure Prediction (CASP) challenges using a diverse set of evaluation metrics. Empirical results demonstrate that the PSCP methods perform well in packing th

SUBMITTER: Vangaru S 

PROVIDER: S-EPMC11888329 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature