Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Videos

REVCOM: a robust Bayesian method for evolutionary rate estimation.

Andrew J Bordner¹, Ruben Abagyan

¹Molsoft LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA. bordner@ornl.gov

Bioinformatics (Oxford, England)

|March 8, 2005

Summary

This study introduces a robust Bayesian method for estimating evolutionary rates, improving conservation predictions for protein sites. The new approach is less sensitive to alignment errors and enhances the reliability of functional site identification.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Pharmacological proximities in the GPCR family discovered using contact-informed amino-acid and binding pocket similarities.

bioRxiv : the preprint server for biology·2026

Same author

A Polypharmacology-Driven Approach to Alzheimer's Disease and Tauopathies: Rational Design, Synthesis and Characterization of Amino-Pyrazole-Based Multikinase (GSK-3β/FYN-α/DYRK1A) Inhibitors.

Journal of medicinal chemistry·2026

Same author

Menthol's disruptive effects on kanamycin-resistant Escherichia coli energy metabolism and ion fluxes.

Biophysical reports·2025

Same author

Structure based design, synthesis and identification of novel covalent reversible dual TLR2/TLR9 small molecule antagonists.

Bioorganic & medicinal chemistry letters·2025

Same author

Identifying Allosteric Small-Molecule Binding Sites of Inactive NS2B-NS3 Proteases of Pathogenic <i>Flaviviridae</i>.

Viruses·2025

Same author

Co-Occurring Infections in Cancer Patients Treated with Checkpoint Inhibitors Significantly Increase the Risk of Immune-Related Adverse Events.

Cancers·2024

Area of Science:

Computational Biology
Bioinformatics
Evolutionary Biology

Background:

Evolutionary conservation analysis predicts functional protein sites but is sensitive to alignment inaccuracies.
Existing methods struggle with local alignment errors, sequence overrepresentation, and unrelated sequences.

Purpose of the Study:

To develop a more robust conservation prediction algorithm.
To reduce sensitivity to common issues in multiple sequence alignments.

Main Methods:

A novel robust constrained Bayesian estimation method for evolutionary rates was developed.
The method was evaluated against an entropy-based measure using 1494 protein interfaces.

Main Results:

The new method demonstrates robustness against alignment variations.

Related Experiment Videos

Approximately 62% of protein interfaces showed significant conservation compared to the surface.

Incorporating alignment reliability reduced arbitrary rate variations.

Conclusions:

The proposed Bayesian method offers a more reliable approach to conservation prediction.
This advancement aids in accurately identifying functional residues and protein interfaces.