COLORADO3D, a web server for the visual analysis of protein structures

Area of Science:

• Structural bioinformatics
• Computational biology
• Protein structure analysis

Background:

• Accurate three-dimensional (3D) protein structure representation is crucial for understanding protein function and interactions.
• Assessing the quality of protein structure models, especially during homology modeling and refinement, presents a significant challenge.

Purpose of the Study:

• To introduce COLORADO3D, a web server for visualizing 3D protein structures with integrated quality assessment and feature mapping.
• To provide a tool that aids in identifying potential structural errors, buried residues, and conserved regions within protein structures.

Main Methods:

• The COLORADO3D server accepts Protein Data Bank (PDB) coordinates and optional multiple sequence alignments as input.
• It utilizes established methods like ANOLEA, PROSAII, PROVE, and VERIFY3D for error detection.
• Output is a PDB-formatted file where the B-factor column is replaced with data on structure quality, residue burial, or sequence conservation.

Main Results:

• COLORADO3D generates PDB files that can be visualized with molecular viewers (e.g., RASMOL) to display 3D clusters of regions with common features.
• The server successfully identified well-folded regions in homology models and guided sequence refinement during the Critical Assessment of Techniques for Protein Structure Prediction (CASP5).

Conclusions:

• COLORADO3D serves as a valuable tool for evaluating protein structure quality at various stages of determination and refinement.
• Its ability to visualize structural features and potential errors enhances the process of protein structure modeling and analysis.