Backbone-dependent rotamer library

Serine backbone-dependent chi1 rotamer populations

Backbone-dependent rotamer library

A backbone-dependent rotamer library is a database of pre-calculated rotamer conformations that are dependent on the backbone conformation of a protein structure. These libraries are used in protein structure prediction and protein design to sample and select appropriate side-chain conformations for a given backbone conformation.

Purpose

The main purpose of a backbone-dependent rotamer library is to provide a set of preferred side-chain conformations for each amino acid residue in a protein structure. By considering the backbone conformation, these libraries can offer more accurate and context-specific rotamer conformations compared to generic rotamer libraries.

Construction

Building a backbone-dependent rotamer library involves analyzing a large dataset of experimentally determined protein structures to identify the relationships between backbone dihedral angles and side-chain conformations. This information is then used to generate a set of rotamer conformations for each amino acid residue at different backbone conformations.

Applications

Backbone-dependent rotamer libraries are widely used in computational methods such as molecular modeling, protein structure refinement, and protein-ligand docking. These libraries help improve the accuracy of predicting protein structures and interactions by providing more realistic side-chain conformations.

See also

• Rotamer
• Protein structure prediction
• Protein design

Template:Rotamer libraries Template:Protein structure prediction