arXiv subjects

Reinhard Schiemann

Publications and source records attributed to Reinhard Schiemann.

2 recordsLinked to original sources

arXiv2005

Exact Enumeration of Three-Dimensional Lattice Proteins

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.

cond-mat.stat-mech↗

arXiv2004

Exact Sequence Analysis for Three-Dimensional HP Lattice Proteins

We have exactly enumerated all sequences and conformations of HP proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the hydrophobic-polar (HP) model, where only two types of monomers are distinguished, we determined and statistically analyzed designing sequences, i.e., sequences that have a non-degenerate ground state. Furthermore we were interested in characteristic thermodynamic properties of HP proteins with designing sequences. In order to be able to perform these exact studies, we applied an efficient enumeration method based on contact sets.

q-bio.BM↗