Tutorial: small-molecule binding site identification

This tutorial identifies binding pockets in the biotin-binding protein streptavidin (PDB 1STP).

You will learn to:

Prerequisites: ADFRsuite 1.0 installed with ADFRsuite-1.0/bin on your PATH, and the tutorial data downloaded.

1. Run AutoSite

AutoSite needs the macromolecule in PDBQT format. Unpack the input file 1STP.pdbqt:

tar zxvf 1STP.tgz

Run AutoSite on it:

autosite -r 1STP.pdbqt
#################################################################
# If you used AutoSite in your work, please cite:               #
#                                                               #
# Pradeep Anand Ravindranath and Michel F. Sanner               #
#                                                               #
# AutoSite: an automated approach for pseudoligands             #
# prediction - From ligand binding sites identification to      #
# predicting key ligand atoms                                   #
#                                                               #
# Bioinformatics (2016)                                         #
#                                                               #
# DOI: 10.1093/bioinformatics/btw367                            #
#                                                               #
# Please see http://adfr.scripps.edu/AutoDockFR/autosite.html   #
# for more information                                          #
#################################################################
AutoSite v1.0.0 started on a Linux-5.11.0-38-generic-x86_64-with-debian-bullseye-sid computer Date Tue Oct 26 10:37:19 2021 computing maps .... No cutoff scan and use cutoffs -0.3 -0.66 -0.5 clustering high affinity points ... analysing 4 clusters ... saving 4 clusters and associated feature points in folder 1STP

clust.| Energy| # of |Rad. of | energy |   bns    |  score |Feature Points
number|       |points|gyration|per vol.|buriedness|v*b^1.5 | D | A | Other
------+-------+------+--------+--------+----------+--------+---+---+------
   1   -112.83   212     4.40    -0.53     0.895    38.64    5   5    9
   2    -67.80   168     4.10    -0.40     0.793    25.78    4   3    9
   3    -45.24   129     3.37    -0.35     0.767    22.53    2   2    8
   4    -44.37   106     3.18    -0.42     0.815    22.14    4   3    6
AutoSite identified and characterized 4 clusters in 1.75 seconds, i.e. 0 hours 00 minutes 01.747343 seconds

AutoSite found 4 clusters (pockets). For each one the table lists its energy, number of points, radius of gyration, energy per volume, buriedness, score, and its feature points by type.

2. Output files

The output files are written in the folder where AutoSite runs.

  • 1STP_AutoSiteSummary.log: the log, with the output printed to the terminal.
  • A folder 1STP/ containing:
    • the cluster points, one PDB file per cluster (1STP._CL.xxx.pdb)
    • the feature points, one PDB file per cluster (1STP_fp_xxx.pdb)
    • a CSV file with the cluster scoring function values for each cluster (1STP_summary.csv)
    • the AutoGrid input file used to compute the grids (rigidReceptor.gpf)
    • the AutoGrid output files (rigidReceptor.glg, rigidReceptor.x.map)
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