Tools of the CPSP package
HPstruct - 3D-lattice structure prediction
HPstruct is a tool to enumerate optimal 3D-lattice structures in the common HP-model. The structures are given in absolute move string representation to describe the structure relatively. Each internal neighboring vector between two monomers along the sequence (an absolute move) is represented by letters. We are using the following encoding:
- F/B = +- x
- L/R = +- y
- U/D = +- z
To calculate the structures a precalculated H-core database is neccessary and used. Currently only a file-based database is available.
The approach uses the generic Gecode constraint programming framework to implement the CPSP method by R. Backofen and S. Will.
To face the highly degenerated structure space of lattice proteins one can exclude symmetric solutions directly. For that, the symmetry breaking approach introduced by S. Will and R. Backofen is used and embedded into the Gecode framework.
In addition, it is possible to constrain the resulting structures. A restriction of the equal absolute move string positions between all structures to a maximal value can be defined or it can be forced that all structures derived by one core differ in at least k monomer positions. Both can be used to get a small set of different samples of the optimal structures if their number is high.
For a complete list of the available parameters run the tool using '-help'.
HPstructSC - structure prediction in side chain models
HPstructSC extends CPSP approach to be utilized within HP side chain models in 3D lattices similar to HPstruct. Within side chain models each amino acid is represented by two monomers, one for the backbone atoms and one representing the side chain atoms. The structure encoding follows the an extended absolute move string encoding:e.g. (U)F(R)D(R)
The absolute positioning of the side chain monomer according to the backbone monomer is given in brackets. Inbetween the absolute positioning of the backbone monomers to each other is given as in the standard HP model.
HPdeg - 3D-lattice degeneracy prediction
The degeneracy of a sequence S is the number of optimal structures that S can adopt in a specific lattice. This can be calculated using the CPSP approach of R. Backofen and S. Will.The resulting tool HPdeg calculates the degeneracy of a given sequence in a specified lattices using the CPSP library.
To handle high degenerated sequences as well and to allow testing for a maximal degeneracy this can be constrained to an upper bound.
For a complete list of the available parameters run the tool using '-help'.
HPoptdeg - Search for low degenerated HP-sequences
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.
For a complete list of the available parameters run the tool using '-help'.
HPoptdegSC - Search for low degenerated HP-sequences
in side chain modelsThe extension of HPoptdeg to side chain HP models in 3D-lattices (see HPstructSC - structure prediction in side chain models)
HPdesign - HP-sequence design for a given structure
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.
For a complete list of the available parameters run the tool using '-help'.
HPnnet - Neutral nets of HP-sequences
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.
For a complete list of the available parameters run the tool using '-help'.
HPrand - Random HP-sequence generation
HPrand generates random HP-sequences of a given length.The number and the H-monomer content of the output sequences can be constrained.
For a complete list of the available parameters run the tool using '-help'.
HPcompress - HP-sequence (de-)compression
HPcompress allows the conversion of HP-sequences between normal/expanded representation and a compressed one.e.g. HHHHPPPPPH <--> 4H5PH
For a complete list of the available parameters run the tool using '-help'.
HPconvert - Lattice structure representation conversion
HPconvert converts lattice structures between different formats.Currently supported representation formats are:
- Absolute move string
- Relative move string
- Absolute monomer positions given in XYZ-file format
The move string representation follows the encoding:
- F/B = +- x
- L/R = +- y
- U/D = +- z
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 #
For a complete list of the available parameters run the tool using '-help'.
HPview - HP lattice protein visualization
HPview creates an output in CML-file format of a sequence/structure that can be viewed with molecule viewers like Chime or Jmol.The structure is NOT validated (if connected and selfavoiding). If it is invalid normal execution cant be guarantied.
The moves are encoded using: F/B : +-x L/R : +-y U/D : +-z
Currently supported viewers are:
For a complete list of the available parameters run the tool using '-help'.