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Table 1 Comparison of AMDock and AutoDock Tools features

From: AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4

Features

AMDock

AutoDock Tools

File formats

Receptor:

pdb, pdbqt

pdb, mol2, pdbq, pdbqs, pdbqt, pqr, cif

Ligand:

pdb, pdbqt, mol2

pdb, pdbq, mol2

Protonation

Receptor:

  

PDB2PQR

Uses the last version 1

Uses PDB2PQR v1.2.1

pH value adjustment

Yes

No (default 7.0)

Experimental protonation state

Only if the user enters a protonated structure 2

Only histidines or when the user enters a protonated structure

Ligand:

  

Open Babel

Uses the last version1

Basic implementation of Open Babel v1.6

pH value adjustment

Yes

No (default value: 7.0)

Structure manipulation

Flexible Side Chains

Not implemented 2

Yes

Flexible Ligand

Active torsions not implemented 2

Yes

Center Automatic 3

Possible binding sites are determined with AutoLigand. Docking is performed for each site.

The user must select a predicted site and prepare the search space. This should be repeated for each site to be tested.

Center on Residues

Centers the box on an AutoLigand object, calculated for a group of selected residues

Only on a selected atom 4

Center on Hetero

Centers the search space in the geometric center of a heteroatom set found in the defined receptor pdb.

On selected heteroatoms or on a ligand 5

Custom Box

Box coordinates defined by the user.

Box coordinates defined by the user.

Box Size

Determined from the radius of gyration of ligand, or set by the user 6

Defined by the user.

Docking programs

AutoDock4

Yes

Yes

AutoDock Vina

Yes

Yes

Docking type

Simple

Yes

Yes

Virtual Screening

No 2

No

Off-target Docking

Yes

No

Covalent Docking

No 2

Yes

Using Autodock4ZN

Yes

Command line

Hydrated docking

No 2

Command line

Analysis of Results

Simple docking

Yes

Yes

Virtual Screening

No2

Yes

Off-target docking

Yes

No

Covalent docking

No 2

Yes

Autodock4 ZN docking

Yes

Yes

Hydrated docking

No 2

Yes

Graphical Visualization

Engine

PyMOL

Python Molecular Viewer

Capacity

All the options included in PyMOL

Protein-ligand interactions and cluster manager for AutoDock4 results

Publication-quality images

Easy high-resolution and custom image generation

Easy low-resolution image generation. Difficult high-resolution image generation

Maintenance

Active development

Inactive

Programming

Python base

Python 2.7.157

Python 2.6 (Inactive development)

Easy to use 8

Docking preparation

1

4

Analysis of Results

2

3

GUI simplicity

1

4

Process Log

1

4

Installation

2

2

Platform

Linux and Windows

Linux, Windows and Mac

  1. 1 Last version with Python 2.x support
  2. 2 Will be available in the next release
  3. 3 A common alternative is to do the so-called blind docking, in which the search space is defined to cover the entire receptor. This involves an increasing in the sampling number so as not to compromise the accuracy of the docking, which leads to an increase in computational cost. Additionally, it can introduce false positives by sampling sites with a different nature than the binding site. Results are usually questionable due to the non-convergence of the scoring functions
  4. 4 We describe the advantages of the method used in AMDock concerning this selection (Fig. 4)
  5. 5 It is possible to select an atom only if the heteroatoms of the receptor have not been removed. After that, these atoms must be removed and the receptor should be redefined. Another possibility is entering a set of heteroatoms and directly select the option “center on ligand”. Both options have limitations and need a deeper understanding of the ADT program
  6. 6 We describe the advantages of the method used in AMDock
  7. 7 Next version in python 3.x under development (https://github.com/Valdes-Tresanco-MS/AMDock-win-py3)
  8. 8 Our own evaluation using a 1–5 scale, where 1 is very easy and 5 is very difficult
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Biology Direct

ISSN: 1745-6150

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