Exploring the lower part of discrete polymer model energy landscapesMichael T. Wolfinger1, Sebastian Will2, Ivo L. Hofacker1, Rolf Backofen2 and Peter F. Stadler3, 4
1 Institute for Theoretical Chemistry, University of Vienna - Währingerstraße 17 A-1090 Wien, Austria
2 Bioinformatics Group, Department of Computer Science, University of Freiburg Georges-Köhler-Allee, Geb. 106, D-79110 Freiburg, Germany
3 Bioinformatics Group, Department of Computer Science, University of Leipzig Härtelstrasse 16-18, D-04107 Leipzig, Germany
4 The Santa Fe Institute - 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
received 21 November 2005; accepted in final form 22 March 2006
published online 14 April 2006
We present a generic, problem-independent algorithm for exploration of the low-energy portion of the energy landscape of discrete systems and apply it to the energy landscape of lattice proteins. Starting from a set of optimal and near-optimal conformations derived from a constraint-based search technique, we are able to selectively investigate the lower part of lattice protein energy landscapes in two and three dimensions. This novel approach allows, in contrast to exhaustive enumeration, for an efficient calculation of optimal and near-optimal structures below a given energy threshold and is only limited by the available amount of memory. A straightforward application of the algorithm is the calculation of barrier trees (representing the energy landscape), which then allows dynamics studies based on landscape theory.
87.15.-v - Biomolecules: structure and physical properties.
87.15.Aa - Theory and modeling; computer simulation.
87.15.Cc - Folding and sequence analysis.
© EDP Sciences 2006