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Other drug discovery tools | Drug discovery

Scaffold Hunter
Desktop

Scaffold Hunter

Allows intuitive hierarchical structuring, visualization and analysis of…

Allows intuitive hierarchical structuring, visualization and analysis of complex structure and bioactivity data. Scaffold Hunter reads data, for example, from biochemical screens, extracts chemically…

Decision Forest
Desktop

Decision Forest

Outperforms decision tree in both training and validation. Decision forest is…

Outperforms decision tree in both training and validation. Decision forest is an ensemble method developed by combining the predictions from multiple independent decision tree models to reach a…

MOSAIC
Dataset

MOSAIC

Gathers information about mapping chemical-genetic (CG interactions) in yeast.…

Gathers information about mapping chemical-genetic (CG interactions) in yeast. MOSAIC includes CG interaction data, mode-of-action predictions and chemical structural information for characterized…

Mona
Desktop

Mona

Allows an intuitive interactive organization and exploration of chemical small…

Allows an intuitive interactive organization and exploration of chemical small molecule datasets on current desktop computer hardware. Mona is a generic, simple, and interactive compound browser and…

CGenFF
Web
Desktop

CGenFF CHARMM General Force Field

Performs atom typing and assignment of parameters and charges by analogy in a…

Performs atom typing and assignment of parameters and charges by analogy in a fully automated fashion. The CGenFF atom typer uses a programmable decision tree. Assignment of bonded parameters is…

NCI ALMANAC
Dataset

NCI ALMANAC A Large Matrix of Anti-Neoplastic Agent Combinations

Allows users to identify combinations with greater antitumor activity than…

Allows users to identify combinations with greater antitumor activity than either agent alone. On the NCI ALMANAC database, promising combinations could be selected for further evaluation in vitro or…

ARQiv-HTS
Desktop

ARQiv-HTS

Prepares and completes whole-organism screening at high-througput rates.…

Prepares and completes whole-organism screening at high-througput rates. ARQiv-HTS includes functions that fall into two categories - those applied to 'Pre-screening Assay Optimization' and…

NetDecoder
Desktop
Web

NetDecoder

A network biology-based computational platform designed to integrate…

A network biology-based computational platform designed to integrate transcriptomes, interactomes and gene ontologies to identify phenotype-specific subnetworks. NetDecoder is based on network flow…

Collector
Desktop

Collector

Allows extraction of data from the ‘Open Pharmacological Space’ (OPS)…

Allows extraction of data from the ‘Open Pharmacological Space’ (OPS) developed by the Open PHACTS project. Collector is an application that extracts series of compounds from OPS, together with…

TiD
Desktop

TiD

Identifies potential drug targets from bacterial proteome. TiD removes…

Identifies potential drug targets from bacterial proteome. TiD removes paralogous proteins, picks essential ones, and excludes proteins homologous with host organisms. It classifies proposed targets…

PaDEL-descripto…
Desktop

PaDEL-descriptor

Calculates molecular descriptors and fingerprints. PaDEL-descriptor was…

Calculates molecular descriptors and fingerprints. PaDEL-descriptor was developed using the Java language and consists of a library and an interface component. It currently calculates 797 descriptors…

iATC-mHyb
Web

iATC-mHyb

Predicts the Anatomical Therapeutic Chemical (ATC) classes. It has been…

Predicts the Anatomical Therapeutic Chemical (ATC) classes. It has been established by hybridizing of the iATC-mISF method with the powerful iATC-mDO sub-predictor. iATC-mHyb outperforms the best…

PubChemQC
Dataset

PubChemQC

Provides a variety and diversity of molecular frameworks. PubChemQC is a…

Provides a variety and diversity of molecular frameworks. PubChemQC is a large-scale molecular electronic structure database based on first-principles quantum chemistry methods. This resource can be…

Chembench
Web

Chembench

Facilitates cheminformatics analyses. Chembench can be used by researchers for…

Facilitates cheminformatics analyses. Chembench can be used by researchers for curation, visualization, analysis, and modelling of chemo-genomics data. It is useful in chemical genomics, drug…

molBLOCKS
Desktop

molBLOCKS

Allows users to break down small molecules into chemically meaningful…

Allows users to break down small molecules into chemically meaningful fragments. molBLOCKS permits analyzing the resulting fragment distribution. It consists of two command-line programs: (1)…

MEPSA
Desktop

MEPSA Minimum Energy Path Surface Analysis

Analyses energy landscapes from a transition state theory perspective. MEPSA…

Analyses energy landscapes from a transition state theory perspective. MEPSA provides features for the identification of all the barriers and minima of the landscape at once and the description of…

3D-MEDNEs
Algorithm

3D-MEDNEs 3D Markovian electron delocalization negentropies

Provides a class of entropy parameters. 3D-MEDNEs offers a physically…

Provides a class of entropy parameters. 3D-MEDNEs offers a physically meaningful 3D generalization of the concept of molecular negentropy by means of stochastic models. The method essentially…

ConfGen
Desktop

ConfGen

Generates bioactive conformers of drug-like molecules. ConfGen is based on the…

Generates bioactive conformers of drug-like molecules. ConfGen is based on the infrastructure from the general molecular modeling program MacroModel. It allows access to multiple all-atom force…

APPLE
Web

APPLE Applying QSAR for Predicting Pan-Inhibitor of Bcl-2 Family Proteins

Predicts a pan- or specific inhibitor for Bcl-2 and Bcl-xL targets. APPLE is a…

Predicts a pan- or specific inhibitor for Bcl-2 and Bcl-xL targets. APPLE is a web-server that classifies the input according to its core and then predicts IC50 from the model generated for the…

Intercalate
Web

Intercalate

Creates the 3D structure of DNA from the DNA sequence along with an…

Creates the 3D structure of DNA from the DNA sequence along with an intercalation site, and docks a ligand at the intercalation site. Intercalate is a state-of-the-art, robust and dedicated drug-DNA…

Mold(2)
Desktop

Mold(2)

Enables the rapid calculation of a large and diverse set of descriptors…

Enables the rapid calculation of a large and diverse set of descriptors encoding 2D chemical structure information. Mold(2) easily and quickly calculates molecular descriptors with no missing values,…

DESMSCI
Dataset

DESMSCI Dragon Exploration System on Marine Sponge Compounds Interactions

Provides information about Marine Sponge Compounds Interactions. DESMSCI is a…

Provides information about Marine Sponge Compounds Interactions. DESMSCI is a public web-based knowledge base that integrates and allows exploration of information about sponge natural products and…

MycPermCheck
Web

MycPermCheck

Serves for knowledge-based estimation of the permeability of potential…

Serves for knowledge-based estimation of the permeability of potential anti-mycobacterial compounds. MycPermCheck is an online tool based on a chemoinformatic data-mining approach. It can be applied…

AutoQSAR
Desktop

AutoQSAR

Permits to build, validate and deploy quantitative structure-activity…

Permits to build, validate and deploy quantitative structure-activity relationship (QSAR) models. AutoQSAR is based on machine-learning methods and encodes current QSAR best practices methods in an…

LEMONS
Desktop

LEMONS Library for the Enumeration of MOdular Natural Structures

Enumerates hypothetical modular natural product structures. LEMONS is an…

Enumerates hypothetical modular natural product structures. LEMONS is an extensible method that allows modification of their monomer composition or tailoring reactions, and comparing of the original…

ArbAlign
Web
Desktop

ArbAlign

Can perform alignments on different automorphism classes based on atom label,…

Can perform alignments on different automorphism classes based on atom label, SYBYL atom type, or atom connectivity. ArbAlign works with an algorithm allowing to find meaningful root-mean-square…

CAPi
Desktop

CAPi

Predicts Apicoplast inhibitors against Plasmodium parasite. CAPi classifies the…

Predicts Apicoplast inhibitors against Plasmodium parasite. CAPi classifies the compounds as inhibitor or non-inhibitor against Plasmodium apicoplast. Five species of Plasmodium can infect and be…

DrugQuest
Web

DrugQuest

A text mining tool to find new associations between drugs. DrugQuest clusters…

A text mining tool to find new associations between drugs. DrugQuest clusters DrugBank records based on their textual information in a multidimensional vector space. We mainly apply partitional…

fraction-who-be…
Desktop

fraction-who-benefit

Uses to learn about the fraction who benefit from a new treatment using…

Uses to learn about the fraction who benefit from a new treatment using randomized trial data. fraction-who-benefit includes (i) proving the plug-in estimator of the bounds can be inconsistent if…

AutoWeka
Desktop

AutoWeka

Allows users to mine data for quantitative structure–activity relationship…

Allows users to mine data for quantitative structure–activity relationship and quantitative structure–property relationships (QSAR/QSPR) studies. Autoweka is a standalone software based on…

ActionPotential
Web
Desktop

ActionPotential

Allows users to perform electrophysiology simulations. ActionPotential is an…

Allows users to perform electrophysiology simulations. ActionPotential is an open source portal, also available as a standalone software, which intends to evaluate the performance of different models…

SMARTS language
Dataset

SMARTS language

Specifies substructural patterns in molecules. The SMARTS line notation is…

Specifies substructural patterns in molecules. The SMARTS line notation is expressive and allows extremely precise and transparent substructural specification and atom typing. SMARTS is related to…

Mirabilis
Web

Mirabilis

Provides an industry-standardised method to predict the purging of potential…

Provides an industry-standardised method to predict the purging of potential mutagenic impurities (PMIs) in a synthetic route based on sound scientific principles. Mirabilis can act as the corporate…

HEDD
Dataset

HEDD Human Epigenetic Drug Database

Focuses on the storage and integration of epigenetic drug datasets that were…

Focuses on the storage and integration of epigenetic drug datasets that were obtained from laboratory experiments that is essential for understanding the mechanism of action of these epigenetic drugs…

Badapple
Web

Badapple Bioassay-data associative promiscuity pattern learning engine

An easy-to-use, readily interpretable algorithm and tool that can assist…

An easy-to-use, readily interpretable algorithm and tool that can assist scientists in navigating a complex scientific and informational landscape. In particular, Badapple is designed for rapid…

MOE
Desktop

MOE Molecular Operating Environment

An integrated drug discovery software. MOE is able to track design ideas and…

An integrated drug discovery software. MOE is able to track design ideas and ligand modifications with property models, produce correlation plots to visualize Structure, Property, Activity…

AZOrange
Desktop

AZOrange

Supports batch generation of quantitative structure-activity relationship…

Supports batch generation of quantitative structure-activity relationship (QSAR) models. AZOrange is based on a simple generalized consensus model. It combines the predictions from the tool’s…

Lab Solvents
Mobile

Lab Solvents

Provides a reference list of solvents, with structures, names, physical…

Provides a reference list of solvents, with structures, names, physical properties, and auxiliary information about their health, safety and environmental impact. Lab Solvents is a reference-card…

Green Solvents
Mobile

Green Solvents

Provides a reference list of solvents, with auxiliary information about their…

Provides a reference list of solvents, with auxiliary information about their health, safety and environmental malignancy, and features for looking them up online. Green Solvents is a simple…

Valence
Mobile

Valence

It provides an interactive visual metaphor for the notions of bonding, whereby…

It provides an interactive visual metaphor for the notions of bonding, whereby atom-localised electrons come together to form covalent bonds, or form lone pair lobes. Valence is an education-focused…

Living…
Mobile

Living Molecules

Allows capturing, archiving and creating of molecular glyphs, which function…

Allows capturing, archiving and creating of molecular glyphs, which function like QR codes for chemical structures, reactions and data. Living Molecules is an iOS application that import chemical…

DSLD
Dataset

DSLD Dietary Supplement Label Database

Contains the full label contents from a sample of dietary supplement products…

Contains the full label contents from a sample of dietary supplement products marketed in the U.S. DSLD contains data from two sources nutrient information taken from dietary supplement labels…

cApp
Desktop

cApp

A Java application that aids handling and storage of information about…

A Java application that aids handling and storage of information about small-molecule compounds. With cApp, the user can appraise compounds with respect to their physico-chemical properties and…

SMSD
Desktop

SMSD Small Molecule Subgraph Detector

Allows users to find the maximum common subgraph (MCS) in small molecules. SMSD…

Allows users to find the maximum common subgraph (MCS) in small molecules. SMSD uses a combination of various algorithms to search the MCS and filters the results in a manner that is chemically…

AtlasCBS
Dataset

AtlasCBS Atlas of Chemico-Biological Space

Allows the exploration of these important areas of drug discovery dynamically…

Allows the exploration of these important areas of drug discovery dynamically online. AtlasCBS can be a useful resource for researchers in the drug discovery process such as: the analysis and…

ABMPred
Web

ABMPred

Predicts antibacterial compounds against MurA enzyme. ABMpred is a server that…

Predicts antibacterial compounds against MurA enzyme. ABMpred is a server that allows user to predict potential inhibitors along with IC50 values using quantitative structure–activity relationship…

J-GLOBAL
Web

J-GLOBAL

Aims to make links, expand and spark linking science and technology…

Aims to make links, expand and spark linking science and technology information. J-GLOBAL provides opportunities to make unexpected discoveries and allows obtain of knowledge from disparate fields…

GPeriodic
Dataset

GPeriodic

Give access to elements from the periodic table.

Give access to elements from the periodic table.

Field-Based…
Desktop

Field-Based QSAR

Allows to optimize lead compounds. Field-Based QSAR integrates exclusively…

Allows to optimize lead compounds. Field-Based QSAR integrates exclusively crude approximations of 3D structure. This tool can explain if the ligand’s electrostatic, hydrophobic, and steric fields…

SARvision |…
Desktop

SARvision | Biologics

Simplifies collaboration work with biopolymers composing unnatural amino acids,…

Simplifies collaboration work with biopolymers composing unnatural amino acids, chemically modified residues, nucleic acids, proteins and peptides. SARvision allows to relate sequence to activity,…

QSite
Desktop

QSite

A molecular simulation method that combines the strengths of the quantum…

A molecular simulation method that combines the strengths of the quantum mechanics (QM) corresponding to the accuracy, and molecular mechanics (MM) corresponding to the speed. QSite is a high…

MacroModel
Desktop

MacroModel

Allows to perform molecular dynamics simulations. MacroModel permits to model…

Allows to perform molecular dynamics simulations. MacroModel permits to model systems at finite temperatures. It is based on stochastic dynamics and mixed Monte Carlo algorithms. The tool computes…

SMP
Web

SMP

Realizes in silico prediction substrate/metabolite specificity. SMP is a web…

Realizes in silico prediction substrate/metabolite specificity. SMP is a web application where predictions are based on Prediction of Activity Spectra for Substances technology (PASS) and Multilevel…

jCompoundMapper
Desktop

jCompoundMapper

Uses as an open source library for molecular fingerprinting with a focus on…

Uses as an open source library for molecular fingerprinting with a focus on machine learning and data mining applications. jCompoundMapper is a library for the decomposition of chemical graphs based…

JChem for…
Desktop

JChem for Office

Integrates structure handling and visualizing capabilities within a Microsoft…

Integrates structure handling and visualizing capabilities within a Microsoft Office environment. JChem for Office allows to make chemistry live in Office application and structures are fully…

KKB
Web
Desktop

KKB Kinase Knowledgebase

Contains kinase structure-activity and chemical synthesis data. KKB represents…

Contains kinase structure-activity and chemical synthesis data. KKB represents a gene-family wide implementation of the Eidogen-Sertanty's web-based technology for the capture, curation, and…

IMoleServer
Desktop

IMoleServer

Helps user to download molecular file from a computer to phone.

Helps user to download molecular file from a computer to phone.

OpenTrialsFDA
Dataset

OpenTrialsFDA

Works on making clinical trial data from the FDA (US Food and Drug…

Works on making clinical trial data from the FDA (US Food and Drug Administration) more easily accessible and searchable. OpenTrialsFDA extracts the relevant data from the FDA documents, link it to…

DemQSAR
Web
Desktop

DemQSAR

A publicly available application for quantitative structure-activity…

A publicly available application for quantitative structure-activity relationship (QSAR) analysis. DemQSAR integrates the open source CDK library to compute various molecular descriptors and…

WENDI
Web

WENDI Web Engine for Non-obvious Drug Information

An integrative data mining tool for drug discovery using aggregate web…

An integrative data mining tool for drug discovery using aggregate web services. WENDI aims to build a full picture of potential biological activities of a chemical compound through the aggregation…

CDPs
Web

CDPs Consensus Diversity Plots

Represents the diversity of chemical libraries considering simultaneously…

Represents the diversity of chemical libraries considering simultaneously multiple molecular representations. CDPs helps the user to compare and classify data sets using diversity metrics. It permits…

PharmGED
Dataset

PharmGED Pharmacogenetic Effect Database

Provides information about the effects of a particular protein polymorphism,…

Provides information about the effects of a particular protein polymorphism, non-coding region mutation, splicing alteration or expression variation on the response of a particular drug. PharmGED…

DDNA
Web

DDNA

Makes an accurate representation of protein-DNA interactions. DDNA is based on…

Makes an accurate representation of protein-DNA interactions. DDNA is based on the distance-scaled, finite ideal-gas reference state (DFIRE) so that it is optimized for protein-DNA interactions. It…

EnzyBase
Dataset

EnzyBase

Gathers information on enzybiotics studies. EnzyBase is an online resource…

Gathers information on enzybiotics studies. EnzyBase is an online resource containing more than 1100 enzybiotics from over 200 natural sources. It provides a platform for current users to…

PharmaTrek
Web

PharmaTrek

Represents an interactive semantic web explorer. PharmaTrek is designed for…

Represents an interactive semantic web explorer. PharmaTrek is designed for researchers in the field of multitarget pharmacology to address complex queries in a most simple and intuitive manner. With…

MoSS
Desktop

MoSS Molecular SubStructure miner

Finds closed frequent fragments of molecules. MoSS models molecules as…

Finds closed frequent fragments of molecules. MoSS models molecules as attributed graphs, thus taking the connection structure though not the 3-dimensional (3D) structure into account. It can be…

FDA Online…
Dataset

FDA Online Label Repository

Represents the most recent drug listing information (the drug labels and other…

Represents the most recent drug listing information (the drug labels and other drug-specific information) that companies have submitted to the Food and Drug Administration (FDA). FDA Online Label…

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