COLORADO-3D

COLORADO-3D maps structural quality, residue burial, and sequence conservation onto three-dimensional protein coordinates to support visualization and assessment of protein models.

Key Features:

• Error Detection: Applies ANOLEA, PROSAII, PROVE, and VERIFY3D to compute residue- and region-level structural quality metrics for error identification.
• Buried Residue Identification: Highlights and scores buried residues to indicate regions not exposed to solvent within the 3D structure.
• Sequence Conservation Depiction: Incorporates multiple sequence alignment data to compute and map sequence conservation values onto the structure.
• B-factor Mapping: Encodes structure quality, residue burial, or conservation values into the PDB-formatted B-factor column.
• Parameter-based Coloring: Colors atoms or residues according to selected parameters to reveal 3D clusters of regions with common features.
• Input Formats: Accepts Protein Data Bank (PDB) coordinate files and optional multiple sequence alignments.

Scientific Applications:

• Structure Quality Assessment: Evaluating protein structures during experimental determination and homology modeling by mapping quality metrics onto 3D coordinates.
• Model Refinement Guidance: Guiding refinement by identifying well-folded and misthreaded regions, as applied by the GeneSilico group during CASP5.
• Visualization of 3D Clusters: Identifying non-adjacent but functionally related regions by coloring structures based on selected parameters.

Methodology:

Accepts PDB coordinate files and optional multiple sequence alignments; applies ANOLEA, PROSAII, PROVE, and VERIFY3D to compute structure-quality metrics, computes residue burial and sequence conservation where applicable, and outputs a PDB-formatted file with the B-factor column replaced by values representing structure quality, residue burial, or conservation levels.