A set of empirical scoring functions for predicting Receptor-Ligand binding affinities (in pKd units): protein-DNA/RNA, protein-small molecule, and protein-protein complexes. Each scoring function was built using generalized linear models (GLMs) applied to specific and curated data sets.
Use github to download (recommmended):
git clone git@github.com:Klab-Bioinfo-Tools/GLM-Score.git
Or if you don't have github installed:
wget https://github.com/Klab-Bioinfo-Tools/GLM-Score/archive/master.zip -O GLM-Score.zip
unzip GLM-Score.zip
cd GLM-Score-master
g++ GLM-Score_0.15.2.cpp -o GLM-Score
cat R/small_molecule/bestGLM.Rdata-a[abc] > R/small_molecule/bestGLM.Rdata
This is an example of how to run GLM-Score:
./GLM-Score ./examples/protein.pdb ./examples/ligand.pdb ./examples/ligand.mol2 DNA
There are 4 input parameters for GLM-Score:
The predicted pKD is shown on the standard output (printed on the terminal screen). For example:
./GLM-Score ./examples/protein.pdb ./examples/ligand.pdb ./examples/ligand.mol2 DNA
3.92735
The command above returned 3.92735 as the predicted pKD.
Additional results are saved in 3 files:
head bonds.log
Hydrogen bonds found: 7
ATOM 1002 N SER A 65 19.354 8.232 25.60
HETATM 4 O BLK 16.520 8.515 25.940
ATOM 202 NH1 ARG A 13 15.904 6.417 21.320
HETATM 9 OXTBLK 16.578 8.524 23.744
ATOM 1011 OG SER A 65 18.347 6.550 23.517
HETATM 9 OXTBLK 16.578 8.524 23.744
(continues)...
head ligand_H-Bonds.pdb
ATOM 184 N ARG A 13 14.993 1.315 25.032
ATOM 185 H ARG A 13 14.308 1.698 25.683
ATOM 186 CA ARG A 13 16.152 2.121 24.667
ATOM 187 HA ARG A 13 16.361 1.835 23.636
ATOM 188 C ARG A 13 17.452 1.819 25.406
ATOM 189 O ARG A 13 18.432 2.551 25.256
ATOM 190 CB ARG A 13 15.815 3.611 24.771
ATOM 191 HB1 ARG A 13 15.327 3.790 25.729
ATOM 192 HB2 ARG A 13 16.744 4.180 24.726
ATOM 193 CG ARG A 13 14.896 4.098 23.662
(continues)...
head ligand.interaction_terms.txt
V2 V3 V4 V5 V6 V7 V18 V19 V20 V21 V22 V23
1016.08 -797.541 8 7 17156.9 735.1 103 33.4077 3.64 91.27 335 11760.7