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 sequenc...

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Bibliographic Details
Published in:The Journal of chemical physics 2005-03, Vol.122 (11), p.114705-114705
Main Authors: Schiemann, Reinhard, Bachmann, Michael, Janke, Wolfhard
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Binding Sites
Computer Simulation
Models, Chemical
Models, Molecular
Models, Statistical
Molecular Sequence Data
Protein Binding
Protein Conformation
Proteins - chemistry
Sequence Analysis, Protein - methods
Structure-Activity Relationship
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Summary: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.
ISSN:0021-9606
1089-7690
DOI:10.1063/1.1814941