CMWeb

CMWeb visualizes and analyzes residue-residue (RR) contact maps derived from protein 3D structures to support protein structure prediction and structural analysis.

Key Features:

• Visualization Capabilities: Displays RR contact maps and links RR contacts to protein 3D structures and multiple sequence alignments for joint inspection.
• Contact Prediction Methods: Integrates five distinct RR contact prediction methods and visualizes predicted and actual RR contacts within the same map.
• Benchmark Testing: Accepts uploads of external RR contact prediction results to enable benchmarking and comparison against reference contacts.
• Statistical Analysis: Computes various contact-related statistics to quantify properties of residue-residue contacts.

Scientific Applications:

• Protein Structure Prediction: Uses RR contact maps and predicted contacts to inform and evaluate protein structure prediction approaches.
• Structural Analysis: Facilitates examination of residue-residue interaction patterns and structural features within protein 3D structures.
• Comparative Studies: Enables comparison of multiple contact prediction methods and uploaded prediction results for method evaluation.

Methodology:

Visualization of contact maps; linking of RR contacts to 3D structures and multiple sequence alignments; integration of five RR contact prediction methods for direct comparison of predicted and actual contacts; support for uploading external prediction results; and computation of contact-related statistics.