HS-Forest on GDT-TS distance

Note: Each decoy must be from the same sequence and have the same number of residues.

1. Introduction
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

3. Usage

hsforest_gdt [OPTION]
    <-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