The COMBREX Project: Design, Methodology, and Initial Results

Abstract

COMBREX (COMputational BRidges to EXperiments, http://combrex.bu.edu) is an NIH-funded enterprise that has brought computational and experimental biologists together, with the goal of greatly improving our overall understanding of microbial protein function [1],[2]. Since its inception, it has made significant progress toward the following goals: identifying the minority of proteins that have already been experimentally characterized, serving as a public repository of novel protein function predictions made by diverse methods, producing a clear chain of evidence from experiment to prediction, identifying (“recommending”) those functional predictions whose verification will contribute most to our overall understanding of protein function, and actually funding the experiments to test function. The recommendation system is a proof of concept based on active learning principles and includes, for a given protein, criteria including phylogenetic distribution of its protein family, biological and clinical phenotypes associated with it, the availability of protein structure data, and its sequence distance from experimentally determined proteins or from the other proteins in its family.