SCit

SCit analyzes and positions protein side-chain conformations by leveraging the relationship between side-chain rotamers and local backbone structures.

Key Features:

• Structural alphabet (four-residue fragments): Describes local backbone conformations using a predefined library of structural prototypes for fragments of four residues.
• Rotameric libraries contingent on backbone conformation: Employs rotameric libraries dependent on local backbone states to predict and position side-chain rotamers.
• Side-chain conformation analysis: Analyzes protein side-chain conformations in the context of surrounding backbone structure.
• Identification of unlikely conformations: Detects side chains with improbable conformations to support structural validation and refinement.
• Side-chain substitution and model generation: Substitutes side chains and generates new protein structures based on predicted rotamers.

Scientific Applications:

• Protein structure analysis: Detects potential inaccuracies in side-chain positioning within experimentally determined protein structures.
• Structural validation and refinement: Aids validation and refinement by identifying improbable side-chain conformations informed by backbone context.
• Structure prediction and protein design: Predicts feasible side-chain conformations to support computational structure prediction and design, including applications in drug design.

Methodology:

Uses a structural alphabet to describe local backbone conformation of four-residue fragments based on a predefined library of structural prototypes; employs rotameric libraries contingent on local backbone conformation to predict and position rotameric side-chain conformations; substitutes side chains to generate new protein structures; and identifies unlikely side-chain conformations by analyzing backbone-dependent rotamer distributions.