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Drug-target interaction detection software tools | Drug discovery

Identification of drug-target interactions is an important process in drug discovery. Although high-throughput screening and other biological assays are becoming available, experimental methods for drug-target interaction identification remain to be…
PharmMapper
Web

PharmMapper

An integrated pharmacophore matching platform with statistical method for…

An integrated pharmacophore matching platform with statistical method for potential target identification. PharmMapper is a freely accessed web-server designed to identify potential target candidates…

PiHelper
Desktop

PiHelper

A drug- and antibody-target information aggregator and provider service.

A drug- and antibody-target information aggregator and provider service.

SEA
Web

SEA Similarity Ensemble Approach

Reveals both expected and unexpected similarities that may be tested by…

Reveals both expected and unexpected similarities that may be tested by examining the ‘off-target’ activities of the ligands themselves. SEA is a web application that reports proteins based on the…

Open Targets
Web

Open Targets

A data integration and visualization platform that provides evidence about the…

A data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. Open Targets platform is designed to support…

Pharos
Web
Desktop

Pharos

A multimodal web interface that presents the data from the Target Central…

A multimodal web interface that presents the data from the Target Central Resource Database (TCRD) which collates many heterogeneous gene and protein datasets. Pharos serves as entry point into the…

PIDGIN
Desktop

PIDGIN Prediction IncluDinG INactivity

Provides a scaled random forest protein target prediction protocol. PIDGIN is a…

Provides a scaled random forest protein target prediction protocol. PIDGIN is a method for the extraction of inactive compounds from PubChem repository. This algorithm enables the oversampling of…

GDISC
Dataset

GDISC Gene-Drug Interaction for Survival in Cancer

Provides a searchable set of survival analyses for the discovery of cancer.…

Provides a searchable set of survival analyses for the discovery of cancer. GDISC contains the integrative analysis on gene copy number data, drug exposure data and survival data of all 32 cancer…

MOST
Desktop

MOST MOst-Similar ligand-based Target

Creates constraint-based models of metabolism, load existing models, export…

Creates constraint-based models of metabolism, load existing models, export models, and run analyses on these models to predict the production of desired compounds by microbes under genetic…

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NSCLC
Desktop

NSCLC Non-Small-Cell Lung Cancer

A computational approach to prioritize candidate drug targets for NSCLC by…

A computational approach to prioritize candidate drug targets for NSCLC by subdividing cell lines into different groups and identifying genetic vulnerabilities targeted to each group. NSCLC uses…

DTI
Web

DTI DrugTargetInspector

Provides an overview of the dataset’s genomic, transcriptomic and proteomic…

Provides an overview of the dataset’s genomic, transcriptomic and proteomic features in a user-friendly way. DrugTargetInspector (DTI) provides a multitude of analysis tools for the identification of…

VacSol
Desktop

VacSol

Automates the high throughput in silico vaccine candidate prediction process…

Automates the high throughput in silico vaccine candidate prediction process for the identification of putative vaccine candidates against the proteome of bacterial pathogens. VacSol rapidly and…

REMAP
Desktop

REMAP

A dual-regularized one class collaborative filtering algorithm for biological…

A dual-regularized one class collaborative filtering algorithm for biological relation prediction. REMAP explores continuous chemical space, protein space, and their interactome on a large scale.…

systemsDock
Web

systemsDock

A web service enabling drug developers to carry out network pharmacology-based…

A web service enabling drug developers to carry out network pharmacology-based prediction and analysis by integrating results from structural biology with systems biology. Its user-friendly GUI…

SELF-BLM
Desktop

SELF-BLM self-training Bipartite Local Mode

Facilitates the identification of potential interactions. SELF-BLM categorizes…

Facilitates the identification of potential interactions. SELF-BLM categorizes unlabeled interactions and negative interactions among unknown interactions using a clustering method. It uses k-medoids…

SwissTargetPred…
Web

SwissTargetPrediction

Allows you to predict the targets of a small molecule. Using a combination of…

Allows you to predict the targets of a small molecule. Using a combination of 2D and 3D similarity measures, it compares the query molecule to a library of 280'000 compounds active on more than…

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mTD
Dataset

mTD MicroRNAs affecting Therapeutic effects of Drugs

Provides comprehensive information about miRNAs affecting drug therapies. mTD…

Provides comprehensive information about miRNAs affecting drug therapies. mTD is a database that provides the sentences describing the drug-miRNA interactions with links to corresponding publications…

PhID
Dataset

PhID

Gathers network pharmacology related interactions information at the systemic…

Gathers network pharmacology related interactions information at the systemic level. PhID aims to provides a repository for visualizing relationships between entities such as drugs, targets,…

IFPTarget
Algorithm

IFPTarget

Enables substantially improved binding pose prediction. IFPTarget is a…

Enables substantially improved binding pose prediction. IFPTarget is a customized virtual target identification method, which uses an interaction fingerprinting (IFP) method for target-specific…

PSDDF
Web

PSDDF Pathogen Specific DNA Drug Finder

Identifies DNA motifs in a selected pathogenic bacterium or virus. PSDDF aims…

Identifies DNA motifs in a selected pathogenic bacterium or virus. PSDDF aims to improve DNA targeted drug discovery by allowing user to target a specific sequence and scan corresponding compounds…

CL
Web

CL Cancer Landscapes

Provides data-derived statistical network models for 8 human cancers. CL…

Provides data-derived statistical network models for 8 human cancers. CL contains several functions for biological interpretability of the network models, such as pathway analysis, drug-target…

Galahad
Web

Galahad

A web-based application for analysis of drug effects. It provides an intuitive…

A web-based application for analysis of drug effects. It provides an intuitive interface to be used by anybody interested in leveraging microarray data to gain insights into the pharmacological…

SLAP
Web

SLAP

A statistical model to assess the association of drug target pairs based on…

A statistical model to assess the association of drug target pairs based on their relation with other linked objects.

AlzPlatform
Web

AlzPlatform

Enables cloud computing and sourcing services and provides powerful…

Enables cloud computing and sourcing services and provides powerful computational algorithms. AlzPlatform is an integrated cloud computing server that assembles a large repertoire of Alzheimer’s…

ChenEtAl2017
Algorithm

ChenEtAl2017

Represents a method for the identification of novel candidate drugs of…

Represents a method for the identification of novel candidate drugs of non-small cell lung cancer (NSCLC). This method consists of three steps: (1) first the extraction of possible compounds by…

ACTP
Web

ACTP Autophagic Compound-Target Prediction

Predicts autophagic targets and relevant pathways for a given compound. ACTP…

Predicts autophagic targets and relevant pathways for a given compound. ACTP permits to explore more possible autophagy-activating or autophagy-inhibiting drugs for potential therapeutic purposes. It…

TargetNet
Web

TargetNet

Makes real-time Drug Target Interaction (DTI) predictions based only on…

Makes real-time Drug Target Interaction (DTI) predictions based only on molecular structures. TargetNet predict the binding of multiple targets for any given molecule, following the spirit of…

PBIT
Web

PBIT Pipeline Builder for Identification of drug Targets

Enables users to access information on all these aspects for studying microbial…

Enables users to access information on all these aspects for studying microbial proteomes. PBIT is an online webserver that has been developed for screening of microbial proteomes for critical…

DeltaNet
Desktop

DeltaNet

A network analysis method for predicting the genetic perturbations caused by a…

A network analysis method for predicting the genetic perturbations caused by a drug or chemical compound using gene expression profiles. DeltaNet is also based on an ordinary differential equation…

SNPLS
Desktop

SNPLS Sparse Network-regularized Partial Least Squares

Identifies combinatorial gene-drug co-modules by integrating gene expression…

Identifies combinatorial gene-drug co-modules by integrating gene expression and drug response data across a set of cell lines as well as a gene interaction network. We first demonstrated the…

DTI Prediction
Desktop

DTI Prediction Drug-Target Interaction Prediction

Discovers new uses for existing drugs. DTI prediction uses complex network…

Discovers new uses for existing drugs. DTI prediction uses complex network theory to predict drug-target interactions (DTI) from a drug-target network. It tends to yield high performance when…

DT-Web
Dataset

DT-Web

Applies a recommendation technique based on bipartite network projection…

Applies a recommendation technique based on bipartite network projection implementing resources transfer within the network. DT-Web contains domain-specific knowledge expressing drugs. It's a…

NetInfer
Desktop

NetInfer

Allows prediction of new potential targets for known drugs, failed drugs and…

Allows prediction of new potential targets for known drugs, failed drugs and new chemical entities on a large scale. NetInfer is a toolkit enabling researchers to input their in-house data and then…

NRLMF
Desktop

NRLMF Neighborhood Regularized Logistic Matrix Factorization

A drug-target interaction prediction algorithm. NRLMF method focuses on…

A drug-target interaction prediction algorithm. NRLMF method focuses on modeling the probability that a drug would interact with a target by logistic matrix factorization, where the properties of…

Drug2Gene
Web

Drug2Gene

Reports relations between genes/proteins and drugs/compounds including…

Reports relations between genes/proteins and drugs/compounds including bioactivity data where available.

DINIES
Web
SuperPred
Web

SuperPred

Connects chemical similarity of drug-like compounds with molecular targets and…

Connects chemical similarity of drug-like compounds with molecular targets and the therapeutic approach based on the similar property principle.

DDR
Desktop

DDR

Assists users in determining drug-target interactions (DTIs). DDR is an…

Assists users in determining drug-target interactions (DTIs). DDR is an efficient DTI prediction method that determines an optimized combination of similarity measures between drugs and between…

ARDnet
Web

ARDnet

Assists users in understanding association and interrelation of age-related…

Assists users in understanding association and interrelation of age-related disorders (ARDs) and associated proteins, pathways, and drugs. ARDnet allows construction of networks of ARDs associated…

VB-MK-LMF
Desktop

VB-MK-LMF Variational Bayesian Multiple Kernel Logistic Matrix Factorization

Predicts drug-target interactions. VB-MK-LMF integrates multiple kernel…

Predicts drug-target interactions. VB-MK-LMF integrates multiple kernel learning, weighted observations, graph Laplacian regularization, and explicit modeling of probabilities of binary drug-target…

GIT
Algorithm

GIT Genetic Interaction network-assisted target Identification

Scores a gene by combining its fitness defect with the screen outcomes of the…

Scores a gene by combining its fitness defect with the screen outcomes of the gene’s neighbors in the genetic interaction network. GIT is a network analysis method for drug target identification. It…

Drug-drug…
Desktop

Drug-drug interaction

Predict unobserved or undetected drug-drug interactions (DDIs). Drug-drug…

Predict unobserved or undetected drug-drug interactions (DDIs). Drug-drug interaction helps to reduce potential risks and understand the mechanism of DDIS. It produces better performances, and the…

DeepDTIs
Desktop

DeepDTIs

Predicts new Drug-Target Interactions (DTIs) between approved drugs and targets…

Predicts new Drug-Target Interactions (DTIs) between approved drugs and targets without separating the targets into different classes. DeepDTIs predicts whether a new drug targets to some existing…

DTINet
Desktop

DTINet

Predicts novel drug-target interactions from the constructed heterogeneous…

Predicts novel drug-target interactions from the constructed heterogeneous network. DTINet captures the context information of individual networks, as well as the topological properties of nodes…

TarPred
Web

TarPred

An online implementation of a recently published computational model for target…

An online implementation of a recently published computational model for target prediction based on a reference library containing 533 individual targets with 179,807 active ligands. TarPred accepts…

KBMF
Desktop

KBMF Kernelized Bayesian Matrix Factorization

Combines kernel-based nonlinear dimensionality reduction, matrix factorization…

Combines kernel-based nonlinear dimensionality reduction, matrix factorization and binary classification for predicting drug-target interaction networks using only chemical similarity between drug…

iDTP
Desktop

iDTP

An integrated structure- and system-based approach of drug-target prediction to…

An integrated structure- and system-based approach of drug-target prediction to enable the large-scale discovery of new targets for small molecules, such as pharmaceutical drugs, co-factors and…

GIFT
Desktop
BalestraWeb
Web

BalestraWeb

An online server that allows users to instantly make predictions about the…

An online server that allows users to instantly make predictions about the potential occurrence of interactions between any given drug-target pair, or predict the most likely interaction partners of…

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ChemiRs
Web

ChemiRs

Integrates and compares ten miRNA target prediction methods of interest.…

Integrates and compares ten miRNA target prediction methods of interest. ChemiRs provides comprehensive features to facilitate both experimental and computational target predictions. In addition,…

CANDO
Algorithm

CANDO Computational Analysis of Novel Drug Opportunities

Determines interactions between protein structures from all organisms and all…

Determines interactions between protein structures from all organisms and all human ingestible compounds. CANDO aims to infer homology of compound/drug at the proteomic scale. It integrates…

CSNAP
Web

CSNAP Chemical Similarity Network Analysis Pull-down

A computational approach for compound target identification based on network…

A computational approach for compound target identification based on network similarity graphs. Query and reference compounds are populated on the network connectivity map and a graph-based neighbor…

nAnnolyze
Desktop
Web

nAnnolyze

An online method that given a compound predicts its protein targets using a…

An online method that given a compound predicts its protein targets using a prebuilt network based on structural similarities. nAnnolyze ranks the predicted targets using a score and two statistical…

idTarget
Web

idTarget

Predicts possible binding targets of a small chemical molecule. Unlike previous…

Predicts possible binding targets of a small chemical molecule. Unlike previous approaches that screen against a specific class of targets or a limited number of targets, idTarget screen against…

TarFisDock
Web

TarFisDock

Identifies drug targets. TarFisDock is a web server that allows to identify…

Identifies drug targets. TarFisDock is a web server that allows to identify potential binding proteins for small molecules such as drugs, lead compounds and natural products. The software docks a…

DePick
Web

DePick

Enables the systematic determination of protein targets linked to phenotypic…

Enables the systematic determination of protein targets linked to phenotypic screen readouts. DePick determines targets specifically linked to chemical phenotypic screens of mammalian organisms. It…

ePlatton
Dataset

ePlatton

Distinguishes polypharmacology and negative drug reactions. ePlatton offers:…

Distinguishes polypharmacology and negative drug reactions. ePlatton offers: (1) library design facility, (2) OMIM disease, KEGG pathway and SIDER drug adverse reaction conditional search and (3)…

StemCellCKB
Dataset

StemCellCKB

Describes the chemical molecules, genes, proteins, and signalling pathways…

Describes the chemical molecules, genes, proteins, and signalling pathways implicated in stem cell regulation. StemCellCKB is a comprehensive domain-specific chemogenomics resource that signals…

Albumin…
Dataset

Albumin binding prediction

Predicts Human Serum Albumin (HAS) binding site of a ligand. Albumin binding…

Predicts Human Serum Albumin (HAS) binding site of a ligand. Albumin binding prediction enables the users (i) to predict if albumin binds the query ligand, (ii) to determine the probable ligand…

DT all
Desktop

DT all

Predicts the drug-target interactions. DT_all is able to enhance the predictive…

Predicts the drug-target interactions. DT_all is able to enhance the predictive accuracies in two scenarios, and the elaborate fusion strategy of multiple classifiers has better predictive power than…

KronRLS-MKL
Desktop

KronRLS-MKL

Models the drug-target interaction problem as a link prediction task on…

Models the drug-target interaction problem as a link prediction task on bipartite networks. KronRLS-MKL allows the integration of multiple heterogeneous information sources for the identification of…

DRABAL
Desktop

DRABAL

Incorporates structure learning of a Bayesian network as a step to model…

Incorporates structure learning of a Bayesian network as a step to model dependency between the high-throughput screening (HTS) assays. DRABAL is a multi-label classification (MLC) solution based on…

BATMAN-TCM
Web
iDrug-Target
Web

iDrug-Target

A package of web-services for predicting drug-target interaction. iDrug-Target…

A package of web-services for predicting drug-target interaction. iDrug-Target contains four predictors: iDrug-GPCR, iDrug-Chl, iDrug-Ezy, and iDrug-NR, specialized for identifying the interactions…

MetaPred
Web

MetaPred

Predicts isoform responsible for metabolizing a drug molecule. MetaPred is a…

Predicts isoform responsible for metabolizing a drug molecule. MetaPred is a web server developed to promote open source software in chemoinformatics. This web application also provides the list of…

iRAISE
Desktop

iRAISE i RApid Index-based Screening Engine

Integrates flexibility of hydrophilic rotatable terminal groups (such as…

Integrates flexibility of hydrophilic rotatable terminal groups (such as hydroxyl groups) of the active site and the query molecule. iRAISE is an inverse screening tool based on the RApid Index-based…

PolyPharma
Mobile

PolyPharma

Provides a variety of modelling and visualisation capabilities that can be…

Provides a variety of modelling and visualisation capabilities that can be applied to molecular structures. PolyPharma is an iOS application that provides a way to view molecular structure-based…

MolTarPred
Web

MolTarPred Molecule Target Prediction

A web server for single protein target fishing exploiting ChEMBL20 data. Once…

A web server for single protein target fishing exploiting ChEMBL20 data. Once the query is submitted on MolTarPred, tanimoto similarities between the Morgan fingerprints of the query molecule and…

DR. PRODIS
Web

DR. PRODIS DRugome PROteome and DISeasome

A comprehensive proteome scale approach that predicts human protein targets and…

A comprehensive proteome scale approach that predicts human protein targets and side effects of drugs. We develop a comprehensive proteome scale approach that predicts human protein targets and side…

KBMF2K
Desktop

KBMF2K

Implements a Bayesian formulation that combines dimensionality reduction,…

Implements a Bayesian formulation that combines dimensionality reduction, matrix factorization and binary classification for predicting drug-target interaction networks using only chemical similarity…

FacPad
Desktop

FacPad

Aims to describe the variation among drug-induced gene expression alternations…

Aims to describe the variation among drug-induced gene expression alternations in terms of a much smaller number of latent factors. FacPad is a Bayesian sparse factor model for the inference of…

DT-Hybrid
Desktop
Web

DT-Hybrid Domain Tuned-Hybrid

An R package that implements the homonymous algorithm for the prediction of…

An R package that implements the homonymous algorithm for the prediction of interactions between small-molecules. Comparison with other recently proposed NBI methods clearly shows that DT-Hybrid is…

HitPick
Web

HitPick

A web server for identification of hits in high-throughput chemical screenings…

A web server for identification of hits in high-throughput chemical screenings and prediction of their molecular targets. HitPick applies the B-score method for hit identification and a newly…

NetPredATC
Desktop

NetPredATC

Predict drug's Anatomical Therapeutic Chemical (ATC)-codes. NetPredATC is…

Predict drug's Anatomical Therapeutic Chemical (ATC)-codes. NetPredATC is a computational method that infer drug’s ATC-codes by integrating its chemical structure and target protein data. The…

T-iDT
Desktop

T-iDT

Discovers possible drug targets in bacterial genomes. T-iDT predicts both…

Discovers possible drug targets in bacterial genomes. T-iDT predicts both essential gene/protein sets as well as target gene/protein sets in a given data set. It can recognize different stringency…

MIND-BEST
Web

MIND-BEST MARCH-INSIDE Nested Drug-Bank Exploration & Screening Tool

Combining MARCH-INSIDE approach and LDA, it is possible to search for an…

Combining MARCH-INSIDE approach and LDA, it is possible to search for an mt-QSAR classifier that can predict with accuracy >94%the probability of drugs to bind more than 300 different drug target…

TargetHunter
Web

TargetHunter

This web portal implements a novel in silico target prediction algorithm, the…

This web portal implements a novel in silico target prediction algorithm, the Targets Associated with its MOst SImilar Counterparts, by exploring the largest chemogenomical databases, ChEMBL.

iGPCR-drug
Web

iGPCR-drug

Predicts the interactions between G protein-coupled receptors (GPCRs) and drugs…

Predicts the interactions between G protein-coupled receptors (GPCRs) and drugs in cellular networking. IGPCR-drug provides a set of steps: (i) construct or select a valid benchmark dataset to train…

drugCIPHER
Desktop

drugCIPHER

Integrates heterogenous drug similarities with protein interation network data…

Integrates heterogenous drug similarities with protein interation network data to accurately predict drug-target relations. drugCIPHER proposes three linear regression models respectively using drug…

MNI
Desktop

MNI Mode-of-action by Network Identification

Differentiates the molecular targets or mediators of the treatment response…

Differentiates the molecular targets or mediators of the treatment response from hundreds of additional genes that exhibit expression changes. MNI employs a machine-learning approach based on…

iCDI-PseFpt
Desktop
Web

iCDI-PseFpt

Identifies the channel-drug interaction in cellular networking with PseAAC and…

Identifies the channel-drug interaction in cellular networking with PseAAC and molecular fingerprints. The overall success rate achieved by iCDI-PseFpt via the jackknife cross-validation was 87.27%,…

GeneOrienteer
Dataset

GeneOrienteer

Gathers information about different types of genes. GeneOrienteer is an online…

Gathers information about different types of genes. GeneOrienteer is an online repository assisting users in the identification of protein-gene interactions. This database using an algorithm that…

MetaILP
Desktop

MetaILP

Assists users in solving drug target discovery problem by exploiting special…

Assists users in solving drug target discovery problem by exploiting special features of metabolic systems. MetaILP is an integer linear programming (ILP) model that can be used to determine the…

HIVfin
Web

HIVfin

Predicts fusion inhibitors against HIV. HIVFin is an in-silico method that can…

Predicts fusion inhibitors against HIV. HIVFin is an in-silico method that can be used for prediction of chemicals as potential fusion inhibitors by targeting Env-mediated entry process. Users can…

SolveBio
Web

SolveBio

Offers intelligent technologies and expertise to guide precision medicine.…

Offers intelligent technologies and expertise to guide precision medicine. SolveBio hosts HIVE, a knowledge network, MESH, an intelligent interface and CORE, a system of technologies. It permits to…

HTDocking
Web

HTDocking

Automates docking procedure to search for protein targets and to explore…

Automates docking procedure to search for protein targets and to explore interactions between compound and protein. HTDocking is a web-based computing tool that was designed and constructed to…

PREDDICTA
Web
insideDNA
Desktop

insideDNA

Uses deep learning, chemogenomics and text mining to accurately predict novel…

Uses deep learning, chemogenomics and text mining to accurately predict novel drug targets or to identify new therapeutic opportunities for advanced compounds. InsideDNA first mines primary genomics…

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…

DrugE-Rank
Desktop

DrugE-Rank

Improves the performance of predicting drug–target interactions of new drugs or…

Improves the performance of predicting drug–target interactions of new drugs or targets. DrugE-Rank aims to take the most advantage of both the feature-based and similarity-based machine learning…

MPD3
Dataset

MPD3 Medicinal Plants Database for Drug Designing

Merges activities of phytochemicals from medicinal plants, their targets and…

Merges activities of phytochemicals from medicinal plants, their targets and literature references. MPD3 contains information about more than 5000 phytochemicals from around 1000 medicinal plants…

Target-Pathogen
Dataset

Target-Pathogen

Facilitates identification and prioritization of candidate targets suitable for…

Facilitates identification and prioritization of candidate targets suitable for new drug development projects. Target-Pathogen is an online resource that allows genome wide based target ranking and…

OCEAN
Web

OCEAN Optimized Cross rEActivity estimatioN

Uses an heuristic approach for the determination of the optimal cutoff for the…

Uses an heuristic approach for the determination of the optimal cutoff for the tanimoto coefficient. OCEAN is an approach for target prediction and poly-pharmacology estimation based on publically…

DASPfind
Web

DASPfind

Infers drug-protein interactions from a heterogeneous graph accompanied with…

Infers drug-protein interactions from a heterogeneous graph accompanied with information about similarities between drugs and similarities between targets. DASPfind relies on finding all simple paths…

ReverseScreen3D
Web

ReverseScreen3D

Predicts the potential protein targets of a query compound of interest.…

Predicts the potential protein targets of a query compound of interest. ReverseScreen3D uses a 2D fingerprint-based method to select a ligand template from each unique binding site of each protein…

Dr. PIAS
Web
DTome
Web

DTome

Constructs drug-target networks. DTome is a web-based tool to search and…

Constructs drug-target networks. DTome is a web-based tool to search and integrate drug-target information to generate a DTome network for the candidate drug(s). The software is efficient in…

inferBind
Desktop

inferBind

A multi-threads C++ package to realize our EM framework to infer the binding…

A multi-threads C++ package to realize our EM framework to infer the binding sites between the drugs and their targets. Both the source codes and complied version can be freely downloaded.

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