Briefings in Bioinformatics, 22(4), 2021, 1–8

https://doi.org/10.1093/bib/bbaa279
Problem Solving Protocol

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InstaDock: A single-click graphical user interface
for molecular docking-based virtual high-throughput
screening
Taj Mohammad †, Yash Mathur† and Md. Imtaiyaz Hassan
Corresponding author: Md. Imtaiyaz Hassan, PhD, FRSB, FRSC, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar,
New Delhi 110025, India. E-mail: mihassan@jmi.ac.in
† These authors contributed equally to this work.

Abstract
Exploring protein–ligand interactions is a subject of immense interest, as it provides deeper insights into molecular
recognition, mechanism of interaction and subsequent functions. Predicting an accurate model for a protein–ligand
interaction is a challenging task. Molecular docking is a computational method used for predicting the preferred orientation,
binding conformations and the binding affinity of a ligand to a macromolecular target, especially protein. It has been
applied in ‘virtual high-throughput screening’ of chemical libraries containing millions of compounds to find potential
leads in drug design and discovery. Here, we have developed InstaDock, a free and open access Graphical User Interface
(GUI) program that performs molecular docking and high-throughput virtual screening efficiently. InstaDock is a single-click
GUI that uses QuickVina-W, a modified version of AutoDock Vina for docking calculations, made especially for the
convenience of non-bioinformaticians and for people who are not experts in using computers. InstaDock facilitates onboard
analysis of docking and visual results in just a single click. To sum up, InstaDock is the easiest and more interactive
interface than ever existing GUIs for molecular docking and high-throughput virtual screening. InstaDock is freely available
for academic and industrial research purposes via https://hassanlab.org/instadock.

Key words: InstaDock; docking tool; protein–ligand interaction; virtual screening; virtual high-throughput screening; drug
discovery; AutoDock Vina; QuickVina-W; docking GUI

Introduction Molecular docking is used to find the most favorable orienta-

Studying protein–ligand interactions using molecular docking is
one of the most widely used approaches in drug development
and discovery [1]. Classically, the process starts with three-
dimensional structures of the known biological target of
therapeutic interest and small molecules of medicinal interest.
tions, binding conformations, strength and binding affinities of
small molecules to a particular target [2]. On one hand, docking
a single molecule is useful in exploring the mechanism of action
of the target and its molecular functions. On the other hand,
virtual screening is used to identify potential molecules by

Taj Mohammad is doctoral candidate working as a senior research fellow at the Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia,
New Delhi, India. His research interests lie in genomic and proteomic analysis over complex diseases, disease modeling, structure-based drug discovery
and NGS analytics.
Yash Mathur is an avid programmer at the Department of Computer Science, Jamia Millia Islamia, New Delhi, India. He codes with Python, Perl, Java and
C++. His areas of interest include computational biology, artificial intelligence and machine learning.
Md. Imtaiyaz Hassan is working as an assistant professor having the distinction of being a fellow of the Royal Society of Biology, UK, and fellow of Royal
Society of Chemistry, UK. He has a vast experience in the area of structure-based drug design and discovery.
Submitted: 14 July 2020; Received (in revised form): 21 September 2020

© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

1
 2 Mohammad et al.
searching and ranking them in certain chemical libraries that
may effectively bind to the target, used in the drug development
process [3] Figure S1.
Several free and commercial docking and virtual screening
programs as Graphical User Interface (GUI) exist [4]. Most of
these programs not only require multiple complementary tools
for each and every task but also require advanced skills in
computers and program handling. In addition, most of the
docking tools do not provide multiple parameters such as
binding affinity, pKi, torsional energy and ligand efficiency in
a single run. It is quite challenging for the non-expert users to
perform molecular docking-based virtual screening directly at
a universal platform, as the process involves a large number of
steps, limiting available GUIs.
InstaDock is a Windows-based platform for docking simu-
lations and virtual screening. It has been developed with the
purpose to resolve the above-mentioned hitches and to make
the GUI user-friendly. It is a single-click executable file that
uses QuickVina-W [5], a modified version of AutoDock Vina for
the docking process [6], and Open Babel for the conversion of
different molecular file formats and coordinates preparation [7].
It uses RasMol version 2.7.5 for visualization purposes [8, 9]
and several custom-made InstaDock algorithms and programs
written in Python for processing and execution.
InstaDock automizes the entire process of molecular docking
and virtual screening procedure in just a single click. It is a versa-
tile application that can be used on several different file formats
of receptors and ligands as input. When the ‘start button’ is
clicked, InstaDock automatically detects the receptor and pro-
cesses it for docking. It generates a search space configuration
(grid) parameter file and subsequently detects the ligands and
processes them to PDBQT format and assigns appropriate atom
types if necessary, in just one go. After docking calculations,
it creates a ‘result folder’ in the working directory, which con-
tains docking results in the form of docked files, affinity scores,
directed top hits and their splitted conformers. It also contains
a brief write-up of the procedure and results for further analysis
and subsequent publication.
Additionally, InstaDock contains different standalone pro-
grams that can be employed for ‘user-directed docking’, virtual
screening and various other individual tasks (Figure 3B). The
tools section of the GUI gives the user the freedom to execute
individual programs, which InstaDock does automatically. Such
as:
(i) Prepare Receptor: It prepares the receptor file from the input
protein found in the working directory.
(ii) Generate Config: It generates a grid parameter file ‘conf.txt’
for the given receptor. If the user wants to create a grid
parameter file for a receptor, he/she just has to go to the
‘Tools’ menu and click the ‘Generate Config’.
(iii) Prepare Ligand(s): It prepares the ligand files for all the
ligands detected in the working directory.
(iv) File Converter: It converts different file formats into PDBQT
files. If the user wants to convert different files into
AutoDock standard format, that is PDBQT, it can be done
by just clicking on ‘File Converter’ in the ‘Additional Tools’
section under the Tools menu and it automatically converts
any standard format (‘.pdb’, ‘.sdf’, ‘.mol’, ‘.mol2’) into
‘.pdbqt’ files.
(v) Hit Identifier: This tool searches for the ‘docked out files’
generated by QuickVina-W/AutoDock Vina and sorts them
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Figure 1. The home window of InstaDock.
based on their binding affinity values and fetches the num-
ber of required hits. It can be used to identify the top hits
from the docking result by just clicking the ‘Hit Identifier’
option in the Additional Tools section under the Tools menu
and entering a reasonable number of hits. It creates a sub-
directory after the user prompt which contains ‘docked out
files’ of the user-supplied hits.
(vi) Vina Splitter (Vina Out-files): It can be used to split all pos-
sible docked conformers from the ‘out files’ generated by
QuickVina-W/AutoDock Vina. If the user wants to split the
Vina-resultant ‘out file’ into possible conformers, one only
has to click on the ‘Vina Splitter’ option in the Additional
Tools section under the Tools menu. This leads to a popup
that allows the user to browse the ligand as per requirement
and then split it into multiple conformers and store them to
a new subdirectory.
(vii) Library Splitter: This tool splits a library of ligands into mul-
tiple files. If the user wants to split a combined library,
he/she just has to click on the ‘Library Splitter’ option in
the Additional Tools section under the Tools menu to split
it into separate ligand files.
(viii) Inspect PDB: It can be used to examine the receptor PDB file
for any inconsistencies that might affect the docking result.
(ix) Visualizer and Complex Maker: It can be used to visualize
the protein–ligand interactions in a three-dimensional view.
This also creates a protein–ligand complex for the job being
visualized, under a subdirectory named ‘Selected Docked
Complex(es)’.
InstaDock suite is a front-end GUI written in Python to
perform docking experiments in Windows-based computers.
It automizes the continuous docking of a large library of small
molecules against a particular target. All predictive and analytic
functions in InstaDock are automated, and the results are
obtained interactively through a user-friendly interface. The
home window of InstaDock is illustrated in Figure 1.
Comparisons with other GUIs
Several docking and virtual screening programs have been devel-
oped and released as GUIs, such as Raccoon [10], PaDEL-ADV
 InstaDock: A single-click molecular docking suite 3

Table 1. A comparison of InstaDock with the common docking GUI programs employing AutoDock Vina

Program Feature∗
Automation ADT Multiple QuickVina-W Visualization OS Write-up
dependency parameters

InstaDock  No    W 
Raccoon × Yes × ×  M ×
PaDEL-ADV × Yes × × × M ×

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PyRx × Yes × ×  M ×
AUDocker LE × Yes  × × W ×
DockingApp × Yes  ×  M ×
EasyDockVina × Yes × × × W ×
MOLA × Yes × × × L ×
DockoMatic × Yes × ×  L ×
VSDK × Yes × × × W ×
∗
Automation: single-click execution; ADT dependency: dependency on AutoDock tools for input file preparation; multiple parameters: generating multiple docking
parameters, such as binding affinity, pKi, torsional energy and ligand efficiency; QuickVina-W: using QuickVina-W for docking calculation; visualization: facilitating
onboard visualization of protein–ligand docked complex; OS: operating system, W—Windows, M—Multiple OS and L—Linux-based OS; write-up: the result summary
of the generated output.

[11], PyRx [12], AUDocker LE [13], VSDocker [14], DockingApp [15],
MOLA [16], DockoMatic [17], etc. Most of these programs have
serious limitations as they require multiple complementary
tools for different tasks, such as receptor preparation, generating
grid parameters, converting different molecular file formats,
ligand preprocessing and visualization. In addition, they are
generally overcomplicated and uninteresting for non-experts.
These programs are restrictive in many aspects with tedious
applications that demand the user to understand the command
prompt and to follow many steps. Typically, they require receptor
and ligand files in AutoDock standard file format, that is PDBQT
to be created through MGL AutoDock Tools (ADT) (https://ccsb.
scripps.edu/mgltools/) [18]. They also require grid parameter
file that contains the search space configuration for a receptor,
to be created using ADT or additional program. InstaDock on
the other hand presents itself as a single-click executable file
that automizes the conventional way of molecular docking
and high-throughput virtual screening. Additionally, it pro-
vides multiple docking parameters such as binding affinity,
pKi, torsional energy and ligand efficiency for a compound
[19]. A comparison of InstaDock with the common docking
GUI programs employing AutoDock Vina has been shown
in Table 1.
Applications of InstaDock
InstaDock aims to be as popular or even go beyond the scope of
available docking programs based on AutoDock Vina. InstaDock
shall be widely used in the modern drug discovery pipeline as
AutoDock Vina is a popular docking program used worldwide
with over 12,000 citations [6]. AutoDock Vina has the highest
binding affinity estimation power (scoring power) among 10
commonly used docking programs [20]. It has higher binding
pose prediction accuracy power (sampling power) than most
of these applications [20]. We have employed QuickVina-W, a
program based on AutoDock Vina, in such a manner that it
can be used for molecular docking and high-throughput virtual
screening by even non-bioinformaticians and people with very
little knowledge of computers. This greatly enhances its scope
of usefulness. We are presenting InstaDock as a tool for docking-
based virtual screening of thousands of ligands against a target
receptor, making it the easiest tool to be used in a structure-
based drug discovery process.
Experimental design
AutoDock Vina and molecular docking
AutoDock Vina is a freely available turnkey docking method that
has been utilized for protein–ligand docking. It is a fast and effec-
tive method designed for generic docking. It works by accepting
receptor and ligand coordinate files for predicting optimally
docked conformations for most systems [6]. Here, in InstaDock,
we have used QuickVina-W, which is created by modifying the
search strategy of AutoDock Vina without modifying the scoring
function nor the interface (input parameters and output format)
and is dedicated to blind docking [5].
InstaDock and virtual screening
Virtual screening is one of the primary applications of molecular
docking. It has numerous accomplishments in the lead discovery
of various therapeutic developments [21]. Virtual screening is
used to screen a large library of compounds in the identification
of high-affinity binding partners of a target receptor for experi-
mental evaluation [22]. InstaDock is a front-end GUI, designed to
simplify the virtual screening steps and analyze the resultant
output. InstaDock uses novel methods created to automatize
the process of computational docking and virtual screening. It
has the capability of docking n number of ligands in an orderly
fashion. Some of the key features of InstaDock consist of the
following:
(i) Executable docking program of QuickVina-W
(ii) Automated detection of target receptor and ligand(s) based
on their content (amino acid and heteroatoms composition)
(iii) Receptor preprocessing, ADT-like coordinates preparation
and config generation
(iv) Preprocessing of ligands and management of their large
collection
(v) Receptor inspection for possible discrepancies that might
affect docking result and provide suggestions
(vi) User choice to provide input files and docking parameters
(vii) Graphical management of jobs and real-time progress bar
(shows screening progress and alerts on pop-up windows)
(viii) Automated retrieval and preprocessing of results
(ix) User-friendly filtering of virtual screening results
 4 Mohammad et al.

(x) Onboard visualization and the complex making of receptor–

ligand interactions
(xi) Exportation of filtered results and post-docking analysis
(facilitates filtering and scoring of ligands and visualization
for protein–ligand interaction analysis)
(xii) A brief write-up of the procedure and result output

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Coordinate preparation for receptor and ligands
Molecular docking needs the user to pay attention to the quality
of the coordinates of the receptor and ligand. InstaDock uses
AutoDock standard Protein Data Bank (PDB) file refined format
termed ‘PDBQT’ that follows united atom representation and a
simplified typing of atoms. InstaDock preprocesses input files
and prepares ADT-like coordinates for the receptor and the
ligands while utilizing Open Babel and a set of custom-made
Python scripts. During ligand preparation, InstaDock considers
ligands to be fully flexible for docking by default; however, users
can supply their ADT-prepared files or even inactive or specify
the torsional degrees of freedom for a molecule.

Search space
InstaDock uses a dynamic custom-made ‘autogrid’ algorithm to
generate grid parameters covering the receptor’s whole space
with an additional margin for blind docking. This algorithm
generates a ‘config file’, which contains the center, and the size
of the grid box for a receptor, calculated using the supplied
coordinates. However, the user can supply their ADT-prepared
grid parameter file ‘conf.txt’ defining the box configuration to Figure 2. Workflow of the InstaDock program that is divided into three major
be searched for site-specific docking. Users can also specify the steps: (i) input of receptor and ligand(s), (ii) docking simulations of the receptor–
ligand system using QuickVina-W and (iii) output containing docking result.
‘maximum number of poses’ to be produced for a ligand and
other parameters in the ‘conf.txt’ file.
InstaDock uses automated scripts for batch processing
of compounds library and receptor. As receptor coordinates
deposited in the PDB often have various issues that need QuickVina-W for protein–ligand docking, Open Babel for
attention. Making sure that only one set of coordinates out molecular conversion and RasMol for molecular visualization.
of the available alternate conformations is selected, including For docking, to predict the protein–ligand interactions and
only the crucial cofactors, is an essential step before docking. their binding affinities, the program first prepares the receptor
Users are also recommended to check that essential residues and ligand files. It then performs the grid-accelerated dock-
or loops are not missing from the coordinates; otherwise, it ing based on a hybrid scoring function and search algorithm
needs remodeling the receptor before going for computational employed in QuickVina-W, originally adopted from AutoDock
docking or virtual screening [18]. InstaDock facilitates the ‘PDB Vina. The program prepared a grid box having blind search
inspection’ function for examining receptor files for possible space parameters with spacing 1.0 Å for the receptor. However,
discrepancies that might affect docking results and suggesting InstaDock can also incorporate the spatial constraints and other
their solutions. parameters provided by the users. Thereafter, the best conform-
ers for every ligand generated by the program are clustered and
ranked by their affinity score. In the virtual screening process,
while extracting the top hits, InstaDock identifies top-ranked lig-
Materials and methods ands based on their binding affinity toward the receptor. Finally,
Hardware, software and start data the top-scoring compounds are separately available for users
in the subdirectory of the ‘results folder’ for further analysis.
(i) Computer: Windows operating system version ‘8’ or ‘higher’
In addition, the docking result can be analyzed by the inbuilt
(ii) Integrated standard programs: QuickVina-W, Open Babel
visualizer available in the Tools menu to identify the key residues
3.3.1 and RasMol 2.7.5
in the protein–ligand binding interface. A typical pipeline for
(iii) Several standalone InstaDock programs written in Python
InstaDock is shown in Figure 2.
(iv) Coordinate files for receptor and ligand (in any standard
format, including PDB, SDF, MOL and MOL2)
Input

Workflow of InstaDock
InstaDock is a tool that integrates several Python programs
developed by us for integration, execution and analysis of
the docking. It uses a few third-party programs, namely
The user is required to put the receptor and ligand files in the
same directory of InstaDock as follows.
(i) Coordinate file for the receptor (in a variety of formats,
including PDB, MOL, MOL2 and SDF)

Figure 3. Post-docking windows of InstaDock. (A) A userprompt after the virtual screening to identify hit molecules. (B) Tools menu consisting of different
standalone programs for individual tasks. (C) Ligand and receptor browser for visualization purposes. (D) A molecular visualization interface for receptor–ligand
interaction analysis.
(ii) Coordinate file for ligand(s) (in a variety of formats, includ-
ing PDB, MOL, MOL2 and SDF)
(iii) Grid parameter file (optional) for user-defined spatial con-
straints and other parameters
Processing
As the user hits the ‘START’ button, the program starts running,
and the job status information is displayed on the ‘progress
bar’ of the ‘home window’ of InstaDock (Figure 1). InstaDock
performs the following tasks immediately after initialization:
(i) Receptor preparation
(ii) Generation of grid parameters for search space
(iii) Ligand(s) preparation
(iv) Docking calculation and scoring
Output
Once the docking calculations are finished, InstaDock prompts
the user to identify the number of the hits (Figure 3A) and creates
a ‘result folder’ containing the following output:
(i) The ‘out-file’ and ‘log-file’ for each ligand in the working
directory
(ii) A ‘CSV’ file containing the binding affinities, pKi, torsional
energy and ligand efficiency for each compound
(iii) Hit(s) and their docked conformers
(iv) A brief write-up for the job
Users can further visualize and analyze the resultant files
while using the inbuilt ‘Visualizer and Complex Maker’ of
InstaDock: A single-click molecular docking suite 5
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InstaDock under the Additional Tools section in the Tools menu
(Figure 3B).
Procedure
Single docking experiment
Place the receptor and ligand files in the same directory as
InstaDock. The receptor and ligand files can be of any standard
chemical format, such as PDB, SDF, MOL, MOL2 or PDBQT. First-
time users are required to install Open Babel 3.3.1 from the ‘Help’
section for file conversion purposes. Hit the START button to
initiate the automatic docking process and wait for the output.
InstaDock performs blind docking by-default for typical lig-
and–protein systems. However, the users can perform docking
as desired by doing several refinement, and defining parameters
in the input files before proceeding for automated docking. To
perform ‘user-directed docking’ as described in this paper, we
recommend users to perform the required steps for a particular
task where they can choose ‘Prepare receptor’, ‘Prepare ligand’
and ‘Generate Config’ options under the Tools menu to create
input files and modify before hitting the START button. If in any
case, a warning pop-up window appears, read the instructions
there and restart the process.
After completion, InstaDock creates a ‘result folder’ in
the working directory containing the docking output and a
brief write-up. It will write a docked coordinate file ‘Ligand-
Name_out.pdbqt’ containing possible docked conformations
and ‘LigandName_log.log’ containing affinity values toward
the target receptor. The docking program gives multiple docked
poses flipped end to end, with highest to lower affinity, based
on the defined number of maximum poses to be produced.
 6 Mohammad et al.
To visualize the results from InstaDock, the inbuilt RasMol
program can be used by just choosing the docked ‘out file’
and the receptor PDB. This will also create a docked complex
of the receptor and the selected ligand. Users can access
this program by clicking the ‘Visualizer and Complex Maker’
tab in the Additional Tools section under the Tools menu
(Figure 3B–D). The protein–ligand complex file can then be found
in a subdirectory named ‘Selected Docked Complex(es)’.
Virtual screening with InstaDock
The process of virtual screening using InstaDock is just the same
as the docking of a single ligand; it is done by placing InstaDock
in the same directory of receptor and ligands and clicking the
START button. If the user provides a single combined library
file of grouped ligands, InstaDock will automatically split the
library into individual ligands and directly uses them for virtual
screening. This also uses the default set of docking parameters
including the grid box with blind configuration. If users want to
screen ligands in a site-specific manner, or defining parameters
in the input files, then they can follow the process described in
the ‘User-directed docking with InstaDock’ section below.
After clicking the START button, the virtual screening process
starts running with real-time status in the progress bar. Once the
virtual screening is finished, it will prompt the user to fetch the
number of hits to be separated and it makes a subfolder under
the ‘Result folder’, containing the top hits and their docked
conformers (Figure 3A). The user can input an integer that rea-
sonably signifies the number of hits to be selected based on the
binding affinity scores, and it will create a subfolder containing
the ‘out files’ of the resultant hit molecules and their splitted
conformers. If the users do not want this process to be executed,
they can just close the window. Users can use this step anytime
in the future to fetch the top hits from the ‘result directory’.
The users can visualize the receptor–ligand interactions by
selecting any docked ligand and the receptor from the directory
and make a docked complex (Figure 3D). The users just have
to choose the docked conformer of the ligand from the results
and the receptor ‘.pdb’ from the working directory and click
‘Visualize’ (Figure 3C).
User-directed docking with InstaDock
InstaDock uses the AutoDock Vina default approach for dock-
ing typical ligand–protein systems [18]. However, one can per-
form ‘user-directed docking’ by doing several refinements and
defining parameters in the input files before proceeding for
docking through InstaDock. For site-specific docking, InstaDock
will require to customize the ‘conf.txt’ by the user to specify
a docking box using ADT covering the receptor binding site
that will be searched. To do this, open ADT and click ‘Grid →
Macromolecule → Open’. ‘Open’ the receptor PDBQT file pre-
pared through InstaDock, and click ‘Yes’ to preserve the existing
charges and ‘OK’ to accept. If a warning window appears alerting
some charges irregularities, just click ‘OK’ to proceed. Go to ‘Grid
→ Grid Box’ to set the size (number of points in x, y and z
dimensions) and center of the search space after defining the
Spacing to 1 Å. Edit ‘conf.txt’ and save in the working directory
and hit the START button of InstaDock to proceed for docking.
For rigid docking or to define ligand flexibility, the user can
supply the ADT-prepared ligand files by specifying the torsional
degrees of freedom in molecules. Users can also inactive or
specify the torsional degrees of freedom in molecules while
using any text editor and opening the ligand files prepared
through InstaDock. To do this, we recommend users to prepare
ligands first from the Tools menu of InstaDock by clicking ‘Tools
→ Prepare Ligands’. Edit the ligand ‘PDBQT’ in any ‘text editor’ by
specifying active torsions, ‘A’ for Active and ‘I’ for Inactive, before
clicking the START button for docking.
InstaDock automatically removes all co-crystallized ligand(s),
water and cofactors from the receptor before docking. The user
can deal with cofactors and/or co-crystallized ligand(s) sepa-
rately by preparing the receptor from the Tools menu of Insta-
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Dock by clicking ‘Additional Tools → File Converter’. This tool
converts the receptor file into ‘.pdbqt’ without removing cofac-
tors and co-crystallized ligands. Edit the receptor ‘.pdbqt’ in any
text editor and click the START button for docking.
For receptor flexibility or docking with flexible side chains,
users need to specify the residue(s) in the receptor to be treated
as flexible. It will need ADT for the preparation of the input files
of the receptor. These files can be supplied in InstaDock for dock-
ing with flexible side chains before hitting the START button. A
step-by-step protocol for customizing ‘conf.txt’ and preparing
input files for performing AutoDock Vina-based docking with
flexible side chains are described elsewhere [18].
Troubleshooting
Possible troubleshooting that may come to users while using
InstaDock is discussed in Table 2.
Result of InstaDock run
After completion, InstaDock provides coordinates for one or
more optimized poses and their binding affinities for the lig-
and(s). The detailed calculated values of all docking terms are
summarized into a ‘CSV’ file. Virtual screening with InstaDock
allows the docking and ranking of thousands of ligands against a
target receptor. Filtering and analyzing is one of the most impor-
tant steps in virtual screening to identify promising leads from
a large library of chemical compounds [23]. InstaDock facilitates
obtaining effective docking results by filtering compounds based
on their binding affinity with the macromolecular target. The
obtained hits can be further analyzed based on their specific
interactions with the critical sites on the receptor and their
drug-like properties. Comprehensive detail on docking analysis
is presented elsewhere [18].
Summary and outlook
Here, we have developed a user-friendly GUI program named
InstaDock for molecular docking and virtual screening of pro-
tein–ligand systems. InstaDock aims to provide a simple and
interactive platform to perform molecular docking and virtual
screening using AutoDock Vina-based program QuickVina-W,
which in itself is a quite difficult task for a non-expert. The fields
of molecular docking and virtual screening are the much-needed
areas of drug discovery, and thus, deployment of InstaDock is
bound to greatly enhance the pre-existing procedures. It is a
novel method that may give users the freedom and efficiency
that is not provided by existing programs. The integration of
various standard programs makes it much more efficient to
perform docking calculation and virtual screening by non-expert
users too. The InstaDock is an on-going project and further
developments will focus on the integration of additional tools
for calculating physicochemical, ADMET and other drug-like
properties of chemical compounds, QSAR and pharmacophore
mapping with automatic molecular modeling.
 InstaDock: A single-click molecular docking suite 7

Table 2. Possible problems and their troubleshooting

S. No. Problem Possible reason Solution

1. InstaDock does not run or InstaDock path setting is Place your working directory in
terminates restricted by the admin account the unrestricted user account (C:
of the system drive) or change your admin
account setting in the system
2. Re-docking do not reproduce the Ligand has too many degrees of Use longer search protocols (by

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affinity and the pose freedom for conformational
search
3. InstaDock shows a popup of Multiple receptors or
multiple receptors receptor–ligand complex(s) in
the working directory
4. InstaDock runs fine but the results There might be multiple reasons
are not as expected for this issue:
There might be multiple chains in
the PDB file provided
There might be missing residues
in the PDB file provided
The ligand file provided may also
give unexpected results. This
could be due to two-dimensional
coordinates in the given file
increasing the maximum
number of binding modes to be
produced using ‘num_modes’ in
the ‘conf.txt’ file) and compare
or simply use the same random
seed as the previous run
Delete or relocate the extra
protein files
Use the ‘Inspect PDB’ tool (under
‘Additional Tools’ section of the
‘Tools’ menu) to check for
inconsistencies in the PDB file
provided
Check for ligand coordinates and
provide three-dimensional
coordinates, if needed

Availability
InstaDock is available through the website: https://www.hassa
nlab.org/instadock.
Key Points
• The available GUIs employing AutoDock Vina to
perform molecular docking and virtual screening
are tedious applications having several serious lim-
itations. They are also quite complex for non-
bioinformatician and people with less knowledge of
computers and program handling.
• InstaDock has been developed as a front-end GUI plat-
form that performs docking simulations and virtual
screening using AutoDock Vina-based QuickVina-W in
just a single click.
• It provides users a straightforward single-click inter-
active platform to perform automated continuous
docking of a database of compounds against prede-
fined protein targets.
• It also provides users the onboard analysis and visu-
alization of the results to identify promising lead
molecules for drug discovery.
• InstaDock calculates multiple parameters for the pro-
tein–ligand system under study, such as free energy of
binding, pKi, torsional energy and ligand efficiency.
Supplementary Data
Supplementary data are available online at Briefings in Bioin-
formatics.
Authorship
Conception and study design: T.M., Y.M. and M.I.H.
Coding and logical programming: T.M. and Y.M.
Data acquisition: T.M. and Y.M.
Writing–original draft: T.M. and Y.M.
Writing–review and editing: T.M. and M.I.H.
Final approval of the manuscript: T.M., Y.M. and M.I.H.
Acknowledgment
T.M. is thankful to the University Grants Commission, India,
for the award of Senior Research Fellowship.
Funding
Indian Council of Medical Research (BIC/12(01)/2015).
Ethical statement
Not applicable.
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