GREMLIN version with residue-residue contact energies from the iPot repo.
git clone https://github.com/gjoni/gremlin3
cd ./gremlin3
make
gremlin- predict protein contact map from an MSAneff- calculate effective number of sequences for an MSArstgen- generate restraints for Rosetta
Usage: ./gremlin3 [-option] [argument]
Options: -i alignment.a3m - input, required
-o matrix.txt - output, optional
-b apcmatrix.txt - output, optional
-n number of iterations 50
-r max gaps per row [0;1) 0.25
-c max gaps per column [0;1) 0.25
-R contact matrix correction
{FN,APC,PROB5,PROB8} PROB8
-t number of threads 1
Usage: ./rstgen [-option] [argument]
Options: -i alignment.a3m - input, required
-m matrix.txt - input, required
-o restraints.txt - output, required
-t restraint type {SIG, BND} SIG
-f fraction of top contacts 1.50 * Len
-p probability cutoff 0.95
-k sequence separation 3
- L-BFGS minimizer by J.Nocedal and N.Okazaki
- ccmpred by J.Soeding group
- iPot statistical potential
[1] H Kamisetty, S Ovchinnikov, D Baker. Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. PNAS (2013). 110:15674–9
[2] S Ovchinnikov, L Kinch, H Park, Y Liao, J Pei, DE Kim, H Kamisetty, NV Grishin, D Baker. Large-scale determination of previously unsolved protein structures using evolutionary information. eLife (2015). 4:e09248
[3] I Anishchenko, PJ Kundrotas, IA Vakser. Contact potential for structure prediction of proteins and protein complexes from Potts model. (2018) Biophys J. DOI: 10.1016/j.bpj.2018.07.035