CaspR

CaspR automates molecular replacement in X-ray crystallography by generating and evaluating multiple homology models from Protein Data Bank (PDB) templates to improve structure solution when sequence identity to templates falls below 35%.

Key Features:

• Automated molecular replacement strategy: Executes an optimized molecular replacement workflow that integrates model generation, MR search, and refinement steps.
• Multiple homology models: Produces a large ensemble of homology models to increase the probability of finding a successful MR solution when individual templates fail.
• Integration with established tools: Uses T-COFFEE for structure–sequence alignments, MODELLER to build homology models, AMoRe for molecular replacement searches, and CNS for model refinement.
• Handles low sequence identity: Specifically addresses decreased MR success rates at sequence identity levels below 35% by testing many alternative models and alignments.
• Input data handling: Accepts experimental diffraction data, target amino acid sequences, and potential template coordinates from the PDB as inputs to the workflow.
• Progress reporting: Produces hierarchically organized summary sheets that report results and metrics for each computational stage.
• Pre-refined structures: Provides pre-refined coordinates for the top-ranking solutions in PDB format to facilitate downstream analysis.

Scientific Applications:

• Structural genomics: Supports large-scale structure-determination pipelines by increasing the fraction of targets amenable to MR.
• Low-homology structure solution: Enables MR-based structure determination for targets with low sequence identity to known templates.
• High-throughput MR screening: Facilitates automated screening of multiple templates and models to identify promising MR solutions for further refinement.

Methodology:

On receipt of experimental diffraction data, target sequences, and candidate templates, CaspR generates structure–sequence alignments with T-COFFEE, builds homology models with MODELLER, performs molecular replacement with AMoRe, and refines models with CNS.