It is therefore embedded in our research field Simplified Protein Models.

For constraint solving the Gecode library is used and needed.

- HPstruct - Optimal structure prediction in 3D-lattices
- HPrep - Equivalence class representatives in 3D-lattices
- HPdeg - Degeneracy of HP-sequences
- HPoptdeg - Search for low degenerated HP-sequences
- HPdesign - HP-sequence design for given structure
- HPnnet - Neutral nets of HP-sequences
- HPrand - Random HP-sequence generator
- HPcompress - HP-sequence (de-)compression
- HPconvert - Lattice structure representation conversion
- HPview - HP-model lattice structure viewer
- HPseq - Converts amino acid into HP sequences

- 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, Rolf Backofen
and Sebastian Will.

Equivalence classes of optimal structures in HP protein models including side chains.

In*Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09)*, 2009. - Martin Mann, Cameron Smith, Mohamad
Rabbath, Marlien Edwards, Sebastian Will,
and Rolf Backofen.

CPSP-web-tool : a server for 3D lattice protein studies.

In*Bioinformatics*,**25**no. 5 pp. 676--677, 2009. - Sebastian Will and Martin Mann.

Counting protein structures by dfs with dynamic decomposition.

In*Proc. of the Workshop on Constraint Based Methods for Bioinformatics*, page 6, 2006. - Rolf Backofen and
Sebastian Will.

A constraint-based approach to fast and exact structure prediction in three-dimensional protein models.

In*Journal of Constraints*,**11**no. 1 pp. 5-30, January 2006. - Sebastian Will.

Exact, Constraint-Based Structure Prediction in Simple Protein Models.

*PhD thesis*, Friedrich-Schiller-Universität Jena, April 2005.

- We provide an extensive Frequently Asked Questions (FAQ) section within our CPSP-web-tools server.
- The online HTML documentation can be found here.
- use 'make doc' in order to create a local copy (needs installed doxygen)
- First steps:

- download, make and install the source
- download the H-core database (or use the included database 'CoreDB')
- run 'HPstruct -dbPath=... -seq=...' for structure prediction
- run 'HPstruct -help' for a list of all program parameters

- the Bioinformatic Utility library - BIU
- the Gecode Constraint Programming library

- (1/2) the CPSP-tool-library source code including
configure scripts

- cpsp-2.4.6.tar.gz
- 2012-02-29 - BIU(2.3.5), Gecode(1.3.0)

Bundle: cpsp-bundle-2.4.6.tar.gz - 2012-02-29 - includes BIU and Gecode library [adjusted to g++ 4.5.3] - cpsp-2.4.5.tar.gz
- 2011-01-19 - BIU(2.3.5), Gecode(1.3.0)

Bundle: cpsp-bundle-2.4.5.tar.gz - 2011-01-19 - includes BIU and Gecode library - cpsp-2.4.4.tar.gz
- 2010-06-25 - BIU(1.3.0), Gecode(1.3.0)

Bundle: cpsp-bundle-2.4.4.tar.gz - 2010-06-25 - includes BIU and Gecode library - cpsp-2.4.2.tar.gz
- 2009-08-18 - BIU(1.3.0), Gecode(1.3.0)

Bundle: cpsp-bundle-2.4.2.tar.gz - 2009-08-18 (update 2010-06-23) - includes BIU and Gecode library - Bundle: cpsp-bundle-2.3.0.tar.gz - 2008-02-25 - includes BIU and Gecode library
- cpsp-2.2.4.tar.gz - 2008-02-10 - BIU(1.3.0), Gecode(1.3.0)
- cpsp-2.1.2.tar.gz - 2007-11-14 - BIU(1.3.0), Gecode(1.3.1)
- cpsp-2.1.0.tar.gz
- 2007-10-22 - BIU(1.3.0), Gecode(1.3.1)

Note: Gecode-1.3.1 crashes on 64-bit systems. Here, you can use Gecode-1.3.0 instead.

Bundle: full cpsp-bundle-2.1.0.tar.gz includes BIU and Gecode library - cpsp-2.0.0.tar.gz
- 2007-07-11 - BIU(1.2.2), Gecode(1.3.1), boost(1.33.x)

Bundle: cpsp-bundle-2.0.0.tar.gz includes BIU and Gecode library - cpsp-1.4.0.tar.gz - 2007-06-18 - BIU(1.1), ELL(0.3.2), Gecode(1.3.1), boost(1.33.x)
- cpsp-1.3.1.tar.gz - 2007-03-29 - BIU(1.1), ELL(0.3.2), Gecode(1.3.1)
- cpsp-1.3.tar.gz - 2007-03-15 - BIU(1.1), ELL(0.3.2), Gecode(1.3.1)
- cpsp-1.2.tar.gz - 2007-03-14 - BIU(1.0), ELL(0.2), Gecode(1.3.0)
- cpsp-1.1.tar.gz - 2006-11-20
- optimal and suboptimal H-cores of size 3-10 are included (needed for HPstruct) - for further cores please use the links below or mail me

- cpsp-2.4.6.tar.gz
- 2012-02-29 - BIU(2.3.5), Gecode(1.3.0)
- (2/2) the optimal and suboptimal H-core data needed for most CPSP-tools

- CPSP_CoreDB.cub.all.tar.gz : all H-cores we have computed for the 3D cubic lattice
- CPSP_CoreDB.fcc.all.tar.gz : all H-cores we have computed for the 3D FCC lattice

For a given HP-sequence HPstruct computes a list of optimal structures (in absolute moves on the lattice) or counts them.

Within the latest extension of the CPSP-package (v2.2.*) we support the prediction of optimal structures in the HP side chain model.

It is possible to generate only one optimal, all optimal, all available structures (limited by the size of the H-core database).

For further H-core files (size 3-10 included) please use the download links provided or mail me.

To get a good sample set for high degenerated sequences one can constrain the solution structures to differ either in x absolute move string positions or lattice positions.

To see the full parameter list run the tool using '-help'.

- Support of side chain models
- Minimal distance for generated structures can be constrained in terms of minimal differences in absolute positions or moves (see documentation)
- Symmetry breaking - no generation or counting of symmetric structures
- Support of cubic and face centered cubic lattice
- Binary neighboring constraints on the lattice
- Global Alldifferent constraint
- Minimal domain initialisation (hulls, P-singlet positions)
- H-core access via file based database
- H-core skipping due to insufficient P-singlet positions
- Cubic H-core skipping due to wrong even/odd position ratio

Here, two structures are defined to be equivalent if they

HPrep enumerates one representative structure for each equivalence class among all optimal structures for a given HP-sequence. The maximal number of structures to enumerate can be restricted.

To see the full parameter list run the tool using '-help'.

For the calculation, the final step of the CPSP-approach of Rolf Backofen and Sebastian Will is used as done for HPstruct.

To handle high degenerated sequences as well and to allow testing for a maximal degeneracy this can be constrained to an upper bound.

To see the full parameter list run the tool using '-help'.

HPoptdeg performs a Monte-Carlo search in the sequence space and finds low degenerated HP-sequences.

To see the full parameter list run the tool using '-help'.

The approach first uses a precalculated database of H-cores to detect sequences that can adopt the structure as an optimal one. Afterwards the degeneracy of the sequences is checked using the CPSP approach of R. Backofen and S. Will.

The level of suboptimal H-cores taken into account can be restricted to speed up the search. If no sequence is found you should increase this level to take more sequences for tests into account.

Additionally, the H-content of the sequence can be constrained in order to restrict the enumerated sequences.

To see the full parameter list run the tool using '-help'.

HPnnet uses for its calculation the CPSP approach of R. Backofen and S. Will in order to check the degeneracy of a sequence neighbor and to compare its optimal structure to X if degeneracy is 1. Per default symmetric structures are excluded but can be included on demand.

To weaken the degeneracy criteria one can increase the maximal value allowed.

To see the full parameter list run the tool using '-help'.

To see the full parameter list run the tool using '-help'.

The structure is NOT validated (if connected and selfavoiding). If it is invalid normal execution can not be guaranteed.

The move string representation follows the encoding:

- F/B = +- x
- L/R = +- y
- U/D = +- z

e.g. HHHHPPPPPH <--> 4H5PH

To see the full parameter list run the tool using '-help'.

Currently supported representation formats are:

- Absolute move string
- Relative move string
- Absolute monomer positions given in XYZ-file format

- F/B = +- x
- L/R = +- y
- U/D = +- z

The XYZ-file format looks like that:

# Beginning with '#' marks a comment line # The lattice positions x,y and z of each point are given # in integer coding e.g. 0 1 0 1 1 0 1 1 -1 # EOF #

To see the full parameter list run the tool using '-help'.

We implemented a certain number of different hydrophobicity tables as listed in CLC bio.