Apr 14 2006 Exploring the Lower Part of Discrete Polymer Model Energy Landscapes

In this paper, we introduce a novel approach to exploring the energy landscapes of discrete polymer models, with a particular emphasis on the lower-energy regions that play a critical role in understanding biopolymer folding behavior

We propose a generic, problem-agnostic algorithm designed for global flooding of the low-energy portions of these landscapes. To demonstrate the effectiveness and versatility of our method, we apply it to lattice proteins in both two and three dimensions as an example application. This innovative algorithm allows to efficiently investigate the complex energy landscapes of discrete systems, providing valuable insights into the topological traits that impact biopolymer folding dynamics.

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

Citation

Exploring the Lower Part of Discrete Polymer Model Energy Landscapes
Michael T. Wolfinger, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Peter F. Stadler
Europhys. Lett. 74(4): 726–32 (2006) | doi:10.1209/epl/i2005-10577-0 | Preprint PDF

Memory Efficient RNA Energy Landscape Exploration
Martin Mann, Marcel Kucharík, Christoph Flamm, Michael T. Wolfinger
Bioinformatics 30: 2584–91 (2014) | doi:10.1093/bioinformatics/btu337 | PDF

BarMap: RNA Folding on Dynamic Energy Landscapes
Ivo L. Hofacker, Christoph Flamm, Michael Heine, Michael T. Wolfinger, Gerik Scheuermann, Peter F. Stadler
RNA 16:1308–16 (2010) | doi:10.1261/rna.2093310 | PDF

Efficient Computation of RNA Folding Dynamics
Michael T. Wolfinger, W. Andreas Svrcek-Seiler, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
J. Phys. A: Math. Gen. 37(17): 4731–41 (2004) | doi:10.1088/0305-4470/37/17/005 | PDF

Barrier Trees of Degenerate Landscapes
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger
Z. Phys. Chem. 216: 155–73 (2002) | doi:10.1524/zpch.2002.216.2.155 | Preprint PDF

Citation

See Also