ConSurf

ConSurf maps evolutionary conservation onto protein and RNA sequences to identify functionally important regions such as ligand-binding and catalytic sites.

Key Features:

• Evolutionary Conservation Analysis: Uses sequence conservation across homologs to pinpoint residues and regions indicative of functional importance.
• Non-redundant Homolog Identification: Identifies non-redundant and sufficiently remote homologs to improve accuracy of conservation estimates.
• RNA Analysis Capability: Extends conservation analysis to RNA molecules while noting that RNA homolog detection can be limited by current database and tool constraints.
• External MSA Importation: Accepts externally prepared multiple sequence alignments (MSAs) to improve homolog sampling and RNA conservation assessment.

Scientific Applications:

• Protein Function Prediction: Highlights conserved residues and regions to support inference of protein functional roles.
• Drug Target Identification: Identifies conserved sites that can be prioritized as potential drug-binding or therapeutic targets.
• Structural Biology Studies: Maps conservation onto structures to inform on residues important for stability and molecular function.

Methodology:

Integrates protein sequence databases and analytical tools to infer evolutionary conservation by analyzing non-redundant homologs; for RNA it provides Basic Protocol 1 (server-based conservation), Basic Protocol 2 (use of external MSAs), and Support Protocols for constructing MSAs using other online servers or locally with nHMMER.