Chain growth algorithms for HP-type lattice proteins
- Deutsches Krebsforschungszentrum, Heidelberg (Germany)
We describe a novel fast straightforward folding algorithm for HP (hydrophobic - polar) type lattice proteins. It is designed after the concept of unguided, cotranslated folding of a nascent peptide. It is deterministic and runs in O(n) in the chain length. Accuracy of prediction is governed by the search depth of the algorithm that is {open_quotes}looked ahead{close_quotes} at each chain growth step. Long range interactions are significantly increased and energy barriers become less prohibitive with increasing search depth. The efficiency of sequential folding is tested and results compared to related methods. All characteristics of the HP-model such as formation of a hydrophobic core and overall compact structures are observed. Since the procedure is very fast and flexible we obtain a useful tool to approximate the sequence to structure mapping of biopolymers in general and to study the complex interplay of folding strategies, potentials and alphabets with large ensembles of random structures. 45 refs., 5 figs.
- Research Organization:
- Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
- OSTI ID:
- 548995
- Report Number(s):
- CONF-970137--
- Country of Publication:
- United States
- Language:
- English
Similar Records
Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model
Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model
Related Subjects
BASIC STUDIES
99 GENERAL AND MISCELLANEOUS
ACCURACY
ALGORITHMS
AMINO ACIDS
BIOLOGICAL EVOLUTION
DNA SEQUENCING
EFFICIENCY
ELECTRONIC STRUCTURE
GENETIC MAPPING
GROWTH
MOLECULAR BIOLOGY
MUTATIONS
ORGANIC POLYMERS
PEPTIDES
PROTEIN STRUCTURE
PROTEINS
RANDOMNESS
STRUCTURAL MODELS
STRUCTURE-ACTIVITY RELATIONSHIPS