CPSP - Constraint-based Protein Structure Prediction
This document provides reference information about the Constraint-based Protein Structure Prediction Approach of Rolf Backofen and Sebastian Will.
The goal
This C++ programming library provides fast and easy extensible implementation of the constraint-based approach of Rolf Backofen and Sebastian Will to predict proven optimal structures of simplified 3D-lattice proteins in the HP-model.Furthermore it will collect additional tools related to this.
CPSP Library Features
- A set of tools for direct 3D-lattice HP-model concerning tasks
- Full library implementation of the CPSP approach of R. Backofen and S. Will
- Interfacing classes to access H-core databases
- Complete API for all classes etc.
Included Tools in 2.3.1
- HPstruct - 3D-lattice structure prediction
- HPstructSC - structure prediction in side chain models
- HPdeg - 3D-lattice degeneracy prediction
- HPoptdeg - Search for low degenerated HP-sequences
- HPoptdegSC - Search for low degenerated HP-sequences
- HPdesign - HP-sequence design for a given structure
- HPnnet - Neutral nets of HP-sequences
- HPrand - Random HP-sequence generation
- HPcompress - HP-sequence (de-)compression
- HPconvert - Lattice structure representation conversion
- HPview - HP lattice protein visualization
- HPviewSC - HP side chain lattice protein visualization
Dependencies
The CPSP depends on the following libraries:
- the Bioinformatic Utility library (BIU) (version 1.3.0)
- the Gecode Constraint Programming Library (version 1.3.0)
Additionally, the documentation also features the following parts:
The following lists and indices are available
- List of all classes including brief documentation
- List of all namespaces including brief documentation
- List of all files
- Class hierarchy
- Alphabetical class index
- Namespace members
- Class members
- File members
Contact : http://www.bioinf.uni-freiburg.de/