Exact Enumeration of Three-Dimensional Lattice Proteins

Details Exact Enumeration of Three-Dimensional Lattice Proteins Exact Enumeration of Three-Dimensional Lattice Proteins

2005-01-17

arxiv.org/abs/cond-mat/0501401v1

Comp. Phys. Commun. 166, 8-16 (2005).

Physics

Condensed Matter

Statistical Mechanics

15pp, elsart.cls, 19 postscript figures, author information under http://www.physik.uni-leipzig.de/index.php?id=22

Scientific paper

10.1016/j.cpc.2004.09.011

We present an algorithm for the exhaustive enumeration of all monomer sequences and conformations of short lattice proteins as described by the hydrophobic-polar (HP) model. The algorithm is used for an exact identification of all designing sequences of HP proteins consisting of up to 19 monomers whose conformations are represented by interacting self-avoiding walks on the simple cubic lattice. Employing a parallelized implementation on a Linux cluster, we generate the complete set of contact maps of such walks.

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