Exact sequence analysis for three-dimensional hydrophobic-polar lattice proteins.
We have exactly enumerated all sequences and conformations of hydrophobic-polar (HP) proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the HP model, where only two types of monomers are distinguished, we determined and statistically analyzed designing sequences, i.e., sequences that have a nondegenerate 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.
Schiemann
Reinhard
R
Institut für Theoretische Physik, Universität Leipzig, Germany. Reinhard.Schiemann@itp.uni-leipzig.de
Bachmann
Michael
M
Janke
Wolfhard
W
D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013329:Structure-Activity Relationship
D011506:Proteins