A simple AutoSite tutorial

In this tutorial we illustrate how to identify binding pockets in the biotin binding protein (PDBID: 1STP).

In this tutorial you will learn:

  • to run AutoSite for a macromolecule
  • to locate and understand the various output file generated by AutoSite.

Prerequisites:

Go back to AutoSite Homepage.

AutoSite requires the macro-molecule to be provided in the PDBQT format. the input file 1STP.pdbqt can be downloaded here (tar zxvf 1STP.tgz).

> autosite -r 1STP.pdbqt

this command will generate the following output

#################################################################
# 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

The output files are created in the folder where the AutoSite program is being run.

The previous command generated a log files containing the output printed to the terminal (1STP_AutoSiteSummary.log).

I addition a folder called 1STP has been created. It contains:

  • a set of files for cluster points (1 per cluster) in PDB format (1STP._CL.xxx.pdb)
  • a set of files for feature points (1 per cluster) in PDB fomat (1STP_fp_xxx.pdb)
  • a CSV file with values of the cluster scoring function for each cluster 91STP_summary.csv)
  • the input file used to calculate grids with AutoGrid (rigidReceptor.gpf)
  • the output files from the AutoGrid calculations (rigidReceptor.glg, rigidReceptor.x.map)