CPSP-tools
CPSP is a collection of tools related to the prediction of optimal structures in simple lattice-protein models like the HP-model. We support the standard backbone models as well as side chain models! It is therefore embedded in our research field Simplified Protein Models. For constraint solving, the Gecode library is used and needed.
For a DIRECT USE check our CPSP web tools Server!
Martin Mann, Sebastian Will, and Rolf Backofen. CPSP-tools - Exact and Complete Algorithms for High-throughput 3D Lattice Protein Studies. BMC Bioinformatics, 9, 230, 2008.
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.
Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, and Rolf Backofen. CPSP-web-tool: a server for 3D lattice protein studies. Bioinformatics, 25, no. 5, pp. 676–677, 2009.
Sebastian Will and Martin Mann. Counting protein structures by dfs with dynamic decomposition. 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. 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.
make doc to create a local copy (needs installed doxygen).CoreDB).HPstruct -dbPath=... -seq=... for structure prediction.HPstruct -help for a list of all program parameters.Note: Optimal and suboptimal H-cores of size 3-10 are included (needed for HPstruct).
HPstruct predicts optimal structures for simple 3D-lattice proteins (HP-model).
It implements the final step of the CPSP-approach of Rolf Backofen and
Sebastian Will.
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’.
HPrep enables the enumeration of equivalence class representatives of
optimal structures. It implements the definitions and methods introduced in
Equivalence classes of optimal structures in HP protein models including side chains.
Here, two structures are defined to be equivalent if they do not differ
in their H-monomer placement. Thus, the equivalence definition follows the
HP energy function that does not constrain P-monomers.
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’.
HPdeg calculates the degeneracy of a given HP-sequence. This is the number
of optimal structures the sequence can adopt in a specific lattice.
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’.
The degeneracy of HP-sequences forms funnel-like structures in the sequence
space. Local search algorithms are therefore a possibility to find local
minima.
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 problem HPdesign is facing is about the design of HP-sequences that fold
optimal into a given structure and have a degeneracy below a given upper bound.
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’.
A neutral net for a given sequence S and its only optimal structure X
includes all sequences S’ that can adopt X as their only optimal structure
too. Additionally, all sequences in S’ have to be direct or indirect
neighbors of S. Two sequences are neighbored if they differ only in one
sequence position.
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’.
HPrand generates random HP-sequence of a given length that can be
constrained in terms of H-monomer content.
To see the full parameter list run the tool using ‘-help’.
HPview creates an output in CML-file format of a sequence/structure that c
an be viewed with molecule viewers like Chime or Jmol. HPview can call such
an external viewer directly.
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:
Currently supported viewers for direct visualization are:
To see the full parameter list run the tool using ‘-help’.
HPcompress allows the conversion of HP-sequences between normal/expanded
representation and a compressed one.
e.g. HHHHPPPPPH <–> 4H5PH
To see the full parameter list run the tool using ‘-help’.
HPconvert converts lattice structures between different formats.
Currently supported representation formats are:
The move string representation follows the encoding:
The given structure is not validated (check if connected and selfavoiding).
For invalid structures a normal tool execution cant be guarantied.
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’.
HPseq implements the method introduced by Kyte and Doolittle (1982) to
derive an HP sequence from a 20 letter code amino acid sequence using
hydrophobicity tables. At each position the average hydrophobicity of
a given span is calculated. Based on a certain threshold the position
is than classified (H)ydrophobic or (P)olar.
We implemented a certain number of different hydrophobicity tables as
listed in CLC bio.