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Structure-based virtual screening software tools | Drug discovery

One of the most widely used techniques for ligand virtual screening is structure-based molecular docking to model the binding pose of a ligand in the binding site of the receptor protein followed by the prediction of binding affinity and/or free…
Raccoon
Desktop

Raccoon

Streamlines the steps of performing a virtual screening and analyzes results.…

Streamlines the steps of performing a virtual screening and analyzes results. Raccoon is a graphical user interface (GUI) that includes (i) automated server connection manager and installation of…

LeadIt
Desktop

LeadIt

Combines major application areas in modern early drug discovery. LeadIt is an…

Combines major application areas in modern early drug discovery. LeadIt is an application that offers an interactive graphical user interface (GUI) which embeds both long-standing and award-winning…

Pharmit
Web
Desktop

Pharmit

Provides an online, interactive environment for the virtual screening of large…

Provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape and energy minimization. Users can import, create and edit…

SiteMap
Desktop

SiteMap

Analyzes and identifies binding sites, and predicts target druggability.…

Analyzes and identifies binding sites, and predicts target druggability. SiteMap studies the druggability of proteins as measured by their ability to bind passively absorbed small molecules tightly.…

ZINCPharmer
Web

ZINCPharmer

An online interface for searching the purchasable compounds of the ZINC…

An online interface for searching the purchasable compounds of the ZINC database using the Pharmer pharmacophore search technology. A pharmacophore describes the spatial arrangement of the essential…

fmcsR
Desktop

fmcsR

Assists in identification of both maximum common substructures (MCSs) and…

Assists in identification of both maximum common substructures (MCSs) and flexible MCSs (FMCSs). fcmsR provides a complete description of subtle similarity patterns shared among compounds. It…

OpenGrowth
Desktop

OpenGrowth

Generates de novo ligands thanks to a growing approach. OpenGrowth is an open…

Generates de novo ligands thanks to a growing approach. OpenGrowth is an open source software that allows users to grow 3D ligands by using statistical analysis of training databases accompanied by…

SUBCOMP
Web

SUBCOMP SUBstructure matching of COMPounds

Compares chemical structures thanks to a subgraph search. SUBCOMP permits to…

Compares chemical structures thanks to a subgraph search. SUBCOMP permits to choose between four databases: Coumpound, Drug, KNApSAck or Reaction. It allows users to highlight the database compounds…

SIMCOMP
Web

SIMCOMP SIMilar COMPound

Compares chemical structures thanks to a graph-based method. SIMCOMP aims to…

Compares chemical structures thanks to a graph-based method. SIMCOMP aims to help in investigate detailed chemical features such as chirality. The application allows users to identify the most common…

GeauxDock
Desktop

GeauxDock

Can take advantage of modern heterogeneous architectures to considerably…

Can take advantage of modern heterogeneous architectures to considerably accelerate structure-based virtual screening applications. GeauxDock is a recently developed molecular docking program. This…

PyGOLD
Desktop

PyGOLD

Allows to automate workflows of any number of steps with any changes required…

Allows to automate workflows of any number of steps with any changes required in the Genetic Optimization for Ligand Docking (GOLD) configuration file. PyGOLD is a comprehensive python based wrapper…

AutoT&T
Web
Desktop

AutoT&T Automatic Tailoring and Transplanting

Generates new ligand molecules from suitable fragments on virtual screening…

Generates new ligand molecules from suitable fragments on virtual screening hits. AutoT&T can automatically lead optimization as well as lead discovery in molecular-targeted drug design. It can…

Protein…
Desktop

Protein Preparation Wizard

Permits to change a raw Protein Data Bank (PDB) structure into all-atom.…

Permits to change a raw Protein Data Bank (PDB) structure into all-atom. Protein Preparation Wizard ensures the accuracy of all downstream modeling simulations. It aims to improve protein and ligand…

MTiOpenScreen
Web

MTiOpenScreen

A web server dedicated to small molecule docking and virtual screening.…

A web server dedicated to small molecule docking and virtual screening. MTiOpenScreen includes two services, MTiAutoDock and MTiOpenScreen, allowing performing docking into a user-defined binding…

HYDE
Desktop

HYDE HYdrogen bond and DEhydration energies

Allows users to calculate molecular surface components. HYDE is based on the…

Allows users to calculate molecular surface components. HYDE is based on the estimation of hydrogen bond and dehydration energies emerging during protein–ligand binding. The functions of this tool…

RADER
Desktop
Web

RADER RApid DEcoy Retriever

Facilitates decoy based assessment of virtual screening. RADER adopts a…

Facilitates decoy based assessment of virtual screening. RADER adopts a database-management regime that supports rapid and large-scale retrieval of decoys, enables high portability of databases, and…

PDEStrIAn
Dataset

PDEStrIAn PhosphoDiEsterase Structure and ligand Interaction Annotated database

A database to revolve around the protein structure of catalytic PDE domains and…

A database to revolve around the protein structure of catalytic PDE domains and the way PDE inhibitors can interact with them. PDEStrIAn is based on the underlying systematic and consistent protocol.…

EGFRpred
Web

EGFRpred

Predicts inhibitors of mutant form of Epidermal Growth Factor Receptor (EGFR).…

Predicts inhibitors of mutant form of Epidermal Growth Factor Receptor (EGFR). EGFRpred provides a web server and a standalone package. Users only needs to submit a scaffold structure along with the…

toolbx_vs
Desktop

toolbx_vs

Allows users to manipulate or modify tasks on a protein complex ensemble.…

Allows users to manipulate or modify tasks on a protein complex ensemble. toolbx_pdb assists users to study structure-based molecular docking. This tool can setup, monitor and analyze a virtual…

RF-Score-VS
Desktop

RF-Score-VS

Provides general purpose and target independent Virtual Screening (VS) tools.…

Provides general purpose and target independent Virtual Screening (VS) tools. RF-Score-VS is a Random Forest-based scoring function which predicts binding affinity. Its descriptors are based on…

TNFPubChem
Web

TNFPubChem

Facilitates the need for the design and virtual screening of novel potent…

Facilitates the need for the design and virtual screening of novel potent small–molecule inhibitors of TNF. TNFPubChem is a ligand-based model developed for the prediction of small-molecule TNF…

Spark-VS
Desktop

Spark-VS

Provides the means to run structure-based virtual screening (SBVS) on public…

Provides the means to run structure-based virtual screening (SBVS) on public cloud resources or on commodity computers clusters. Spark-VS is the implementation of a method that permits to define…

DockBlaster
Web

DockBlaster

A fully automated docking system including self-assessment. DockBlaster is…

A fully automated docking system including self-assessment. DockBlaster is tested for pose-fidelity, the ability to reproduce experimentally observed poses within some tolerance limit, and…

Np-likeness
Desktop

Np-likeness Natural product-likeness

Calculates Natural Product (NP)-likeness of a molecule, i.e. the similarity of…

Calculates Natural Product (NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. NP-likeness is a useful criterion to screen…

ToxDBScan
Web

ToxDBScan

Scans the TG-GATEs and DrugMatrix databases for similar chemicals, given the…

Scans the TG-GATEs and DrugMatrix databases for similar chemicals, given the deregulated genes after short-term treatment with a chemical in male rats. ToxDBScan is a web application that allows user…

e-LEA3D
Web

e-LEA3D

A first web server to perform computer-aided de novo drug design, to build…

A first web server to perform computer-aided de novo drug design, to build focused combinatorial libraries of molecules and to perform virtual screenings. The de novo drug design tool creates new…

AHTpin
Web

AHTpin

Designs antihypertensive (AHTs) peptides. AHTpin is a user-friendly platform…

Designs antihypertensive (AHTs) peptides. AHTpin is a user-friendly platform providing various options to the users for predicting, designing and screening of AHT peptides. This web application…

fpocket
Web

fpocket

An open source protein pocket (cavity) detection algorithm based on Voronoi…

An open source protein pocket (cavity) detection algorithm based on Voronoi tessellation.

LigandBox
Dataset

LigandBox LIGANDs Data Base Open and eXtensible

Contains purchasable chemical compounds for the purpose of drug development.…

Contains purchasable chemical compounds for the purpose of drug development. LigandBox is a 3D chemical compound library available for efficient structure-based virtual screening with a maximum…

KNIME-Extension…
Desktop

KNIME-Extensions

Provides a method to researchers in order to develop, validate, and deploy…

Provides a method to researchers in order to develop, validate, and deploy multi-step computational workflows. KNIME Extensions supplies a solution for scientists searching for a way to combine…

LiSIs
Web

LiSIs Life Sciences Informatics

Facilitates the discovery of cancer chemopreventive agents. LiSIs uses numerous…

Facilitates the discovery of cancer chemopreventive agents. LiSIs uses numerous methods like RDKit, R or AutoDock Vina. It can proceed a lot of operations such as molecular descriptor calculation,…

AuPosSOM
Web
Desktop

AuPosSOM Automatic analysis of poses using self-organizing maps

Evaluates docking results based on the clustering of compounds by the…

Evaluates docking results based on the clustering of compounds by the similarity of their contacts with the receptor. AuPosSOM represents a good alternative to the energy-based scoring functions for…

Panther
Desktop

Panther

An ultrafast multipurpose docking tool. In Panther, a simple…

An ultrafast multipurpose docking tool. In Panther, a simple shape-electrostatic model of the ligand-binding area of the protein is created by utilizing the protein crystal structure. The features of…

SwissParam
Web

SwissParam

A fast force field generation tool able to generate, for arbitrary small…

A fast force field generation tool able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field (MMFF), but in a functional form that is…

DrugEBIlity
Web

DrugEBIlity

Evaluates the suitability of the binding site for small molecules. DrugEBIlity…

Evaluates the suitability of the binding site for small molecules. DrugEBIlity is a web resource that allows user to search with a sequence, a Protein Data Bank (PDB) code, or to upload a structure.

Shape Screening
Desktop

Shape Screening

Allows shape-based superposition and similarity searching. Shape Screening is a…

Allows shape-based superposition and similarity searching. Shape Screening is a software for lead optimization studies, and can also be used in the early stages of lead discovery. The software can…

Screening…
Desktop

Screening Assistant

Stores and analyzes small to very large chemical libraries. Screening Assistant…

Stores and analyzes small to very large chemical libraries. Screening Assistant stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers…

iScreen
Web

iScreen

A cloud-computing system for traditional Chinese medicine (TCM) intelligent…

A cloud-computing system for traditional Chinese medicine (TCM) intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by…

VAMMPIRE
Dataset

VAMMPIRE

Informs about structure-based drug design and optimization.

Informs about structure-based drug design and optimization.

iDrug
Web

iDrug

A versatile web server for both pharmacophore- and similarity-based virtual…

A versatile web server for both pharmacophore- and similarity-based virtual screening and target identification to facilitate computational drug discovery. The interface is easy-to-use and can be…

GSA
Desktop

GSA GPU-accelerated structure similarity algorithm

Speeds the performance of structure similarity search for over two orders of…

Speeds the performance of structure similarity search for over two orders of magnitude faster. GSA is a GPU-accelerated structure similarity algorithm based on atom center fragment (ACF) approach.…

ALiBERO
Desktop

ALiBERO

Takes over the steps of the LiBERO framework. ALiBERO starts from single or…

Takes over the steps of the LiBERO framework. ALiBERO starts from single or multiple receptor structures and creates receptor ensembles, performs virtual screening (VS) docking and selects the…

IVSPlat
Desktop

IVSPlat

Allows users to manage virtual screnning (VS) and to analyze VS results.…

Allows users to manage virtual screnning (VS) and to analyze VS results. IVSPlat performs many practical virtual screening tasks derived from UCSF Dock and PharmaGist. It offers users a visualization…

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