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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
Published on: February 10, 2023
The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures
Ofir Goldenberg1, Elana Erez, Guy Nimrod
1Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel.
Nucleic Acids Research
|October 31, 2008
Summary
ConSurf-DB provides evolutionary conservation analysis for proteins in the Protein Data Bank (PDB). This resource helps identify key residues in functionally important protein regions by visualizing evolutionary patterns on 3D structures.
Area of Science:
- Structural bioinformatics
- Computational biology
- Evolutionary biology
Background:
- The Protein Data Bank (PDB) contains a vast collection of protein structures.
- Understanding protein function often requires analyzing evolutionary conservation patterns.
- Identifying functionally important residues is crucial for protein engineering and drug design.
Purpose of the Study:
- To present ConSurf-DB, a comprehensive repository for evolutionary conservation analysis of PDB proteins.
- To provide a tool for visualizing conservation patterns on 3D protein structures.
- To facilitate the identification of functionally important residues.
Main Methods:
- Collecting sequence homologues for each PDB entry.
- Aligning collected sequences using standard bioinformatics methods.
- Calculating amino acid position conservation using the Rate4Site algorithm, incorporating phylogenetic information and stochastic evolutionary processes via empirical Bayesian inference.
Main Results:
- ConSurf-DB offers evolutionary conservation scores for amino acid positions within PDB proteins.
- The Rate4Site algorithm assigns conservation levels based on phylogenetic relationships and evolutionary rates.
- Visualizing conservation on 3D structures aids in identifying key residues within functional regions.
Conclusions:
- ConSurf-DB is a valuable, regularly updated resource for studying protein evolutionary conservation.
- The repository aids researchers in pinpointing functionally critical amino acids by mapping conservation onto protein structures.
- This approach enhances the understanding of protein function and evolution.
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