HPstruct implements the CPSP approach, as introduced by Backofen and Will (Constraints, 2006), to predict provably optimal structures of 3D lattice proteins in the HP-model. For a given HP-sequence S and a given lattice type (cubic or face centered cubic), (all) optimal structures are calculated. The CPSP approach computes the global minimal energy for S, too.
HPstruct - Optimal structure prediction
Try HPstruct with these examples:
When using HPstruct please cite :
- Martin Mann, Sebastian Will, and Rolf Backofen
CPSP-tools - Exact and Complete Algorithms for High-throughput 3D Lattice Protein Studies.
In BMC Bioinformatics, 9, 230, 2008.
- Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, and Rolf Backofen.
CPSP-web-tools: a server for 3D lattice protein studies.
Bioinformatics, 25 (5), 676-677, 2009.
- Martin Mann, Rolf Backofen, and Sebastian Will.
Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains.
Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009.
- Rolf Backofen and Sebastian Will.
A constraint-based approach to fast and exact structure prediction in three-dimensional protein models.
Journal of Constraints, 11 (1), 5-30, 2006.
Results are computed with HPstruct version 2.4.6 linking Gecode 1.3.0 and BIU 2.3.6