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

v1.1.1: Apr 3, 2012. Improved parameters description.
v1.1: Mar 30, 2012. Fixed a bug in printing error messages when an input file is missing.
v1.0: Dec 8, 2011. First released version.

1. Linux binary


Decompress: tar xvfz hsforest.X.bin.tar.gz
X: version number

2. Source code


Decompress: tar xvfz hsforest.X.tar.gz
X: version number

3. Data_sets

4. Usage

hsforest [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 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" without parameters.


hsforest -i my_list -R my_pivots -B 10_best -o output -r 40 -h 20 -t 20

5. HS-Forest on GDT-TS