HS-Forest on GDT-TS distance
Note: Each decoy must be from the same sequence and have the same number of residues.
HS-Forest on GDT-TS distance integrates the Fortran implementation of GDT-TS score in TMscore. It requires g++ and gfortran installed on your system to compile. Since a GDT-TS score is more time-consuming to compute than RMSD, the overal runtime of HS-Forest on GDT-TS is significantly slower than the RMSD version.
2. Source code
Decompress: tar xvfz hsforest_gdt.tar.gz
<-i> A file listing the absolute path to each decoy.
<-R> A file listing the absolute path to each pivot decoy. Should be selected randomly.
<-B> A file listing the absolute path to the 10 best energy decoy. The file can contain between 1 and 10 decoys.
<-o> Output file for top decoys (sorted).
<-r> Number of pivots to sample from pivots in pivot file. Recommend value: between 20 and 60.
<-h> H_max value. Recommended value: half of the value of the <-r> parameter.
<-t> Number of trees. Recommended value: between 15 and 30.
[-S] (Optional) Number of largest clusters to consider. Default value: 30.
This usage information is also available when typing "hsforest_gdt" without parameters.
hsforest_gdt -i my_list -R my_pivots -B 10_best -o output -r 40 -h 20 -t 20