CooPPS - A system for the
Cooperative Prediction of Protein Structures
CooPPS is a system for the
cooperative prediction of protein structures. It allows a suitable set of
prediction tools to be chosen, out of a given set of available ones, so as to maximize
the overall performances on the given prediction problem.
It works in three phases:
- Definition of the Application Domain; it is a set of proteins whose structure
is known which define the domain of interest
- Team Building; in this phase, all the prediction tools are required to
provide a prediction for the proteins in the Application Domain; each of them
is evaluated and some precision measures are computed. Finally, the best team
for the Application Domain is composed by considering the set of predictors
best performing, cooperatively, on the Application Domain (The two phases above
must be carried out only once until the user wants to change the application
domain)
- Prediction; after the team is composed, CooPPS is able to predict proteins
whose structure is not known. It first queries the predictors in the team for
their predictions and, then, integrates their results by considering their
accordance and their precision
For any question, please
contact terracina@mat.unical.it
Referencing this work,
please cite:
L. Palopoli and G.
Terracina, CooPPS: A System for the Cooperative Prediction of Protein
Structures, Journal of Bioinformatics and Computational Biology, 2(3), 471-496, 2004
The code is made freely
available for academic and non-commercial uses only.
To download and use CooPPS:
Click
here for a Windows version (tested)
System requirements:
- Java Virtual Machine
1.4.1 ( http://java.sun.com )
Instructions:
Unzip the files and run
CooPPS.exe
Click
here for a platform independent version (not completely tested)
System requirements:
- Java virtual machine
1.4.1 ( http://java.sun.com )
Instructions:
- If you have installed
java in the directory /java you must set the path to /java/bin
- Unzip the CooPPS files
- If you unzipped the
CooPPS files in the directory /CooPPS, the classpath must contain the
following entries:
/CooPPS;
/CooPPS/CooPPS_prediction;
/CooPPS/interfax;
/CooPPS/mail.jar;
/CooPPS/activation.jar;
- run java Show
We gratefully thank Francesco Strangio for his efforts in the software development