Publications - Published papers

Please find below publications of our group. Currently, we list 496 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

Exploring the Lower Part of Discrete Polymer Model Energy Landscapes

Michael T. Wolfinger, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Peter F. Stadler

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Europhys. Lett. 74: 726-732 (2006).

Abstract


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 calculation of barrier trees (representing the energy landscape), which then allows dynamics studies based on landscape theory.

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87.15.-v Biomolecules: structure and physical properties, 87.15.Aa Theory and modeling; computer simulation, 87.15.Cc Folding and sequence analysis