Robetta

Robetta predicts protein structures and evaluates mutation impacts by combining comparative modeling, de novo Rosetta fragment insertion, RosettaNMR with NMR constraints, and computational interface alanine scanning.

Key Features:

• Sequence parsing and domain identification: Parses input amino acid sequences and identifies potential domains for modeling.
• Homology detection: Identifies homologous structures using BLAST, PSI-BLAST, FFAS03, and 3D-Jury.
• Comparative modeling: Builds models based on identified templates from existing structural databases.
• De novo structure prediction: Constructs models de novo using the Rosetta fragment insertion method by assembling small peptide fragments guided by known folding patterns and energetics.
• NMR integration (RosettaNMR): Integrates experimental NMR constraints to refine de novo structure predictions via RosettaNMR.
• Mutation analysis (interface alanine scanning): Performs computational interface alanine scanning to predict effects of residue mutations on protein-protein binding affinity and to identify interaction hotspots.

Scientific Applications:

• Protein tertiary structure prediction: Generation of protein structural models using comparative and de novo approaches.
• Modeling without homologs: De novo modeling for sequences lacking suitable homologous templates using Rosetta fragment insertion.
• NMR-guided refinement: Refinement of structural models by incorporating experimental NMR constraints via RosettaNMR.
• Mutation impact assessment: Evaluation of mutation effects on protein-protein interactions and identification of critical interface residues through computational alanine scanning.

Methodology:

Parses sequences into domains; detects homologs with BLAST, PSI-BLAST, FFAS03, and 3D-Jury; performs comparative modeling using template structures from databases; generates de novo models via Rosetta fragment insertion assembling peptide fragments guided by folding principles and energetics; integrates NMR constraints through RosettaNMR; conducts computational interface alanine scanning to assess mutation effects.