Modeling of protein side-chain conformations with RASP

Methods Mol Biol. 2014:1137:43-53. doi: 10.1007/978-1-4939-0366-5_4.

Abstract

Modeling of side-chain conformations on a fixed protein backbone, also called side-chain packing, plays an important role in protein structure prediction, protein design, molecular docking, and functional analysis. RASP, or RApid Side-chain Predictor, is a recently developed program that can model protein side-chain conformations with both high accuracy and high speed. Moreover, it can generate structures with few atomic clashes. This chapter first provides a brief introduction to the principle and performances of the RASP package. Then details on how to use RASP programs to predict protein side-chain conformations are elaborated. Finally, it describes case studies for structure refinement in homology modeling and residue substitution.

MeSH terms

  • Models, Molecular*
  • Molecular Conformation*
  • Proteins / chemistry*
  • Software*
  • Web Browser

Substances

  • Proteins