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Open Access Research article

An adaptive bin framework search method for a beta-sheet protein homopolymer model

Alena Shmygelska1 and Holger H Hoos2*

Author Affiliations

1 Department of Structural Biology, Stanford University, 299 W. Campus Dr., Stanford, CA 94305, USA

2 Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC V6T 1Z4, Canada

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BMC Bioinformatics 2007, 8:136  doi:10.1186/1471-2105-8-136

Published: 24 April 2007

Abstract

Background

The problem of protein structure prediction consists of predicting the functional or native structure of a protein given its linear sequence of amino acids. This problem has played a prominent role in the fields of biomolecular physics and algorithm design for over 50 years. Additionally, its importance increases continually as a result of an exponential growth over time in the number of known protein sequences in contrast to a linear increase in the number of determined structures. Our work focuses on the problem of searching an exponentially large space of possible conformations as efficiently as possible, with the goal of finding a global optimum with respect to a given energy function. This problem plays an important role in the analysis of systems with complex search landscapes, and particularly in the context of ab initio protein structure prediction.

Results

In this work, we introduce a novel approach for solving this conformation search problem based on the use of a bin framework for adaptively storing and retrieving promising locally optimal solutions. Our approach provides a rich and general framework within which a broad range of adaptive or reactive search strategies can be realized. Here, we introduce adaptive mechanisms for choosing which conformations should be stored, based on the set of conformations already stored in memory, and for biasing choices when retrieving conformations from memory in order to overcome search stagnation.

Conclusion

We show that our bin framework combined with a widely used optimization method, Monte Carlo search, achieves significantly better performance than state-of-the-art generalized ensemble methods for a well-known protein-like homopolymer model on the face-centered cubic lattice.