I-TASSER-MR

I-TASSER-MR performs automated molecular replacement by generating and editing I-TASSER-derived full-length protein models and searching/refining their placements against X-ray crystallographic data to determine phases for distant-homology proteins.

Key Features:

• Iterative Fragment Assembly: Generates full-length protein models from primary amino acid sequences using I-TASSER's iterative structural fragment reassembly.
• Progressive Sequence Truncation: Refines models via progressive sequence truncation based on local variations observed during structural assembly simulations.
• MR-REX Integration: Uses MR-REX with replica-exchange Monte Carlo simulations to search for optimal placements of models within crystal unit cells.
• Phase Refinement with CNS: Refines phases and performs atomic model refinement and selection using CNS (Crystallography & NMR System).
• Inputs: Accepts primary amino acid sequences and raw crystal diffraction data as inputs.
• Outputs: Produces annotated phase information and refined structural models suitable for downstream analysis.
• Phasing Parameters: Allows specification of B-factor setting methods and the number of models used for phasing.
• Performance: Solves approximately 36% more targets compared to using the best threading templates.

Scientific Applications:

• Molecular replacement for low-sequence-identity targets: Enables MR for proteins with low sequence identity to available templates in X-ray crystallography.
• Distant-homology structure determination: Expands the range of proteins amenable to X-ray crystallographic analysis by improving phase determination for distant-homology proteins.

Methodology:

Generate full-length models with I-TASSER iterative fragment reassembly; apply progressive sequence truncation to edit models; submit edited models to MR-REX using replica-exchange Monte Carlo for placement searches; refine phases and atomic models with CNS.