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Ligand-based virtual screening software tools | Drug discovery

FTrees
Desktop

FTrees Feature Trees

Handles and searches large virtual combinatorial libraries. FTrees performs…

Handles and searches large virtual combinatorial libraries. FTrees performs similarity searches in the generated Fragment Space. It stores the physicochemical properties of the substructure…

FlexS
Desktop

FlexS

Superposes pairs of molecules and takes full flexibility of one of the…

Superposes pairs of molecules and takes full flexibility of one of the structures into account. FlexS serves for superimposing pairs of ligands, one of which is treated as flexible (test ligand) and…

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…

USR-VS
Web

USR-VS

A USRbased webserver for large-scale prospective virtual screening. USR-VS…

A USRbased webserver for large-scale prospective virtual screening. USR-VS performs large-scale ligand-based Virtual Screening (VS), which is oriented to the prospective validation of the obtained…

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…

DOVIS
Desktop

DOVIS DOcking-based VIrtual Screening

Automates docking jobs with AutoDock. DOVIS is a utility software and a Linux…

Automates docking jobs with AutoDock. DOVIS is a utility software and a Linux cluster-based application that can reliably screen millions of compounds against a receptor and automatically save the…

Neural Network…
Desktop

Neural Network scoring

Aids the computational identification of small-molecule ligands. NNscore is…

Aids the computational identification of small-molecule ligands. NNscore is based on a neural-network scoring function and provides a single estimate of the pKd. It attempts to simulate, albeit…

SwissSimilarity
Web

SwissSimilarity

A web tool for rapid ligand-based virtual screening (LBVS) of small to…

A web tool for rapid ligand-based virtual screening (LBVS) of small to ultralarge libraries of small molecules. SwissSimilarity offers the possibility to perform LBVS on more than 30 chemical…

DOCKTITE
Desktop

DOCKTITE

Allows covalent docking and virtual screening in molecular operating…

Allows covalent docking and virtual screening in molecular operating environment (MOE). DOCKTITE combines the knowledge-based scoring function drug score extended (DSX) and the empirical scoring…

MedusaScore
Algorithm

MedusaScore

Allows to evaluate protein-ligand binding. MedusaScore is a scoring function…

Allows to evaluate protein-ligand binding. MedusaScore is a scoring function that describes the protein-ligand binding using physical interaction model. The function includes an explicit…

Induced Fit
Desktop

Induced Fit

Accounts for receptor flexibility in ligand-receptor docking by iteratively…

Accounts for receptor flexibility in ligand-receptor docking by iteratively combining rigid receptor docking with protein structure prediction and refinement. Induced Fit generates viable receptor…

MLViS
Web

MLViS Machine Learning-based Virtual screening tool

Classifies molecules as drug-like and nondrug-like molecules. MLViS is based on…

Classifies molecules as drug-like and nondrug-like molecules. MLViS is based on various machine learning methods, including discriminant, tree-based, kernel-based, ensemble and other algorithms.…

Blaze
Server

Blaze

Uses 3D molecular fields to make particularly suitable for scaffold hopping.…

Uses 3D molecular fields to make particularly suitable for scaffold hopping. Blaze is a ligand based virtual screening tool. It helps to: (i) increase the diversity of project leads and backups, (ii)…

PASS Targets
Web
Desktop

PASS Targets

Predicts interactions between protein targets and drug-like compounds. PASS…

Predicts interactions between protein targets and drug-like compounds. PASS Targets is able to predict interactions of drug-like compounds with 2507 protein targets from different organisms based on…

CancerIn
Web
Desktop

CancerIn

Predicts anticancer potency of an unknown molecule and its GI50 across…

Predicts anticancer potency of an unknown molecule and its GI50 across different cancer cell lines. CancerIN is a web server that consists of three modules for designing, library screening and…

LigQ
Web

LigQ

Aids the researcher in the selection and preparation of ligands-as well as the…

Aids the researcher in the selection and preparation of ligands-as well as the desired protein receptor-for a Virtual Screening (VS) procedure. The LigQ web based tool is divided in four…

HybridSim-VS
Web

HybridSim-VS

Allows large-scale ligand-based Virtual Screening (VS). HybridSim-VS combines…

Allows large-scale ligand-based Virtual Screening (VS). HybridSim-VS combines two-dimensional (2D) fingerprint- and tri-dimensional (3D) shape-based similarity search methods. It is a general hybrid…

VSPrep
Desktop

VSPrep

Permits the preparation of molecules for virtual screening. VSPrep is a…

Permits the preparation of molecules for virtual screening. VSPrep is a comprehensive protocol designed adapted to different types of compounds such as macrocycles and flexible molecules. It is…

mRAISE
Desktop

mRAISE m RApid Index-based Screening Engine

Provides biologically relevant molecular alignments of the ligands. mRAISE is a…

Provides biologically relevant molecular alignments of the ligands. mRAISE is a tool for ligand-based virtual screening based on the RApid Index-based Screening Engine (RAISE) technology. The…

LigMatch
Desktop

LigMatch

Ranks databases of chemical compounds. LigMatch is a virtual screening (VS)…

Ranks databases of chemical compounds. LigMatch is a virtual screening (VS) method which uses a geometric hashing method to compare database compounds with the 3D bioactive conformation of a template…

KiDoQ
Web

KiDoQ

Provides prediction of antibacterial compounds against dihydrodipicolinate…

Provides prediction of antibacterial compounds against dihydrodipicolinate synthase (DHDPS). KiDoQ is an approach for prediction of antibacterial compounds that both take quantitative…

wwLigCSRre
Web

wwLigCSRre

Performs ligand-based screening using a 3D molecular similarity engine.…

Performs ligand-based screening using a 3D molecular similarity engine. wwLigCSRre provides an online versatile facility to assist the exploration of the chemical similarity of families of compounds.…

pepMMsMIMIC
Web

pepMMsMIMIC

A web-oriented peptidomimetic compound virtual screening tool based on a…

A web-oriented peptidomimetic compound virtual screening tool based on a multi-conformers three-dimensional (3D)-similarity search strategy. Key to the development of pepMMsMIMIC has been the…

UFSRAT
Web

UFSRAT Ultra-fast Shape Recognition with Atom Types

An efficient algorithm that considers both the 3D distribution (shape) and…

An efficient algorithm that considers both the 3D distribution (shape) and electrostatics of atoms to score and retrieve molecules capable of making similar interactions to those of the supplied…

ElectroShape
Web

ElectroShape

Enables any user to estimate polypharmacology profiles and side effects of…

Enables any user to estimate polypharmacology profiles and side effects of compounds based on the molecular similarity concept. ElectroShape is a method that compares the distance and charge…

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…

MolClass
Desktop
Web

MolClass

Generates computational models from user-defined small molecule datasets based…

Generates computational models from user-defined small molecule datasets based on structural features identified in hit and non-hit molecules in different screens. Each new model is applied to all…

LBVS
Web

LBVS Ligand-Based Virtual Screening

An online platform for ligand-based virtual screening using publicly accessible…

An online platform for ligand-based virtual screening using publicly accessible databases. LBVS adopts Bayesian learning approach to create virtual screening models because of its noise tolerance,…

NoiseMaker
Desktop

NoiseMaker

Creates in silico simulated high throughput screening data sets for use in…

Creates in silico simulated high throughput screening data sets for use in testing and selecting appropriate statistical techniques for quality determination and hit identification. NoiseMaker can be…

CATSlight2
Web

CATSlight2 Chemically Advanced Template Search

A web server for molecular similarity searching. Note that CATSlight2 does not…

A web server for molecular similarity searching. Note that CATSlight2 does not allow for full database searching. A collection of up to 100 compounds may be uploaded by the user for similarity…

LigMerge
Desktop

LigMerge

A package which provides a fast and easy way to generate molecular models…

A package which provides a fast and easy way to generate molecular models derived from known inhibitors without the need for information about the receptor. LigMerge algorithm creates novel compounds…

TLR4HI
Web

TLR4HI

Calculates a percent inhibitory value of the compound against TLR4. TLR4hi…

Calculates a percent inhibitory value of the compound against TLR4. TLR4hi server predicts the inhibitory activity of chemical entity. It also helps in finding new molecule by generating analogs of…

GDoQ
Web

GDoQ

Provides valuable information about protein-ligand interaction. GDoQ provides…

Provides valuable information about protein-ligand interaction. GDoQ provides an open source platform to the scientific community for discovering new drugs against bacterial target…

Core Hopping
Desktop

Core Hopping

Allows the rapid screening of novel cores to help overcome unwanted properties…

Allows the rapid screening of novel cores to help overcome unwanted properties by generating new lead compounds with improved core properties while preserving key R-group interactions. Core Hopping…

LigPrep
Desktop

LigPrep

Generates energy minimized 3D molecular structures. LigPrep can correct Lewis…

Generates energy minimized 3D molecular structures. LigPrep can correct Lewis structures by applying sophisticated rules. It eliminates mistakes in ligands to reduce downstream computational errors.…

USRCAT
Desktop

USRCAT Ultrafast Shape Recognition with CREDO Atom Types

Provides a solution to the lack of atom type information in the ultrafast shape…

Provides a solution to the lack of atom type information in the ultrafast shape recognition (USR) algorithm. Researchers, particularly those with only limited resources, who wish to use ligand-based…

ViCi
Web

ViCi

An innovative software tool for ligand-based drug design. ViCi uses a…

An innovative software tool for ligand-based drug design. ViCi uses a combination of mathematical descriptors of molecular size, shape and topology to describe small molecule structures. Following…

ValLigURL
Web

ValLigURL

It can be used by practising crystallographers to validate the geometry of a…

It can be used by practising crystallographers to validate the geometry of a ligand and to compare the conformation of a ligand with all instances of that ligand in the structural database (wwPDB).…

ChemMapper
Web

ChemMapper

Explores target pharmacology and chemical relationships against any given small…

Explores target pharmacology and chemical relationships against any given small molecules. ChemMapper is a versatile web-based tool that assembles a large repertoire of bioactive chemical database…

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