ipot_solver

A program for solving the inverse Potts problem

Installation

git clone https://github.com/gjoni/ipot_solver
cd ipot_solver
make

Usage

Usage:   ./ipot_solver [-option] [argument]

Options:  -i input.txt                   - input, required
          -o output.txt                  - output, optional
          -c checkpoint.txt              - input/output, optional
          -n number of iterations          100
          -t number of threads             1

Example

Learn energy parameters for the AACE18 statistical contact potential:

gunzip example/graph.txt.gz
./ipot_solver -i example/graph.txt -t 4 -n 20 -o table.out

Links

• iPot statistical contact potential
• libLBFGS: a library of Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS)

References

I Anishchenko, PJ Kundrotas, IA Vakser. Contact potential for structure prediction. of proteins and protein complexes from Potts model. (2018). Biophys J. 115(5):809-21