iPot

iPot (from inverse Potts) - a set of programs to calculate inter- and intra- protein contact energies using atom-atom and residue-residue statistical contact potentials derived from the Potts model [1].

aace18    - atomic contact energies (18 atom types from Ref. [2])
aace20    - atomic contact energies (20 types, all heavy atoms in a residue belong to one type)
aace167   - atomic contact energies (167 types, all heavy atoms in a residue belong to different types)
rrce20    - contact energies between residue centroids

aace18 with default parameters should be sufficient for most applications.

Installation

Program download and compilation

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

Download contact potentials database (optional)

wget http://vakser.compbio.ku.edu/main/downloads/ipot_data.tar.gz
tar xf ipot_data.tar.gz

Usage

By the example of aace18 (other programs have the same interface):

Usage:   ./aace18 [-option] [argument]

Options:  -r receptor.pdb \  # PDB file with receptor's coordinates
          -l ligand.pdb \    # (optional) PDB file with ligand's coordinates
          -t table.txt \     # (optional) aace18 contact potential table 
          -d dmax            # (optional) contact distance, default dmax=6.8A

Intrachain energy:

./aace18 -r example/1i2m_u1.pdb

Interchain energy:

./aace18 -r example/1i2m_u1.pdb -l example/1i2m_u2.pdb

Interchain energy using non-default energy table:

./aace18 -r example/1i2m_u1.pdb -l example/1i2m_u2.pdb -t /path/to/database/ipot_data/AACE18/table.8.0A_k4 -d 8.0

Links

• Vakser Lab
• kdtree library by John Tsiombikas
• ipot_solver - inverse Potts solver

References

[1] 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

[2] C Zhang, G Vasmatzis, JL Cornette, C DeLisi. Determination of atomic desolvation energies from the structures of crystallized proteins. (1997) J Mol Biol. 267(3): 707-6