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Workflow systems

There has been huge progress in the open cheminformatics field in both methods and software development. Unfortunately, there has been little effort to unite those methods and software into one package.Source text:(Wojcikowski et al., 2015) Open…
UNICON
Desktop

UNICON

Encapsulates an important conversion functionality from the NAOMI software…

Encapsulates an important conversion functionality from the NAOMI software library in a single command-line tool. UNICON is a consistent chemical model that aims for the appropriate representation of…

3D-e-Chem-VM
Desktop

3D-e-Chem-VM

Integrates cheminformatics and bioinformatics tools for the analysis of…

Integrates cheminformatics and bioinformatics tools for the analysis of protein−ligand interaction data. 3D-e-Chem-VM is an open source, freely available Virtual Machine that consists of software…

ChemSAR
Web

ChemSAR

Provides a comprehensive modelling pipeline by integrating six model generation…

Provides a comprehensive modelling pipeline by integrating six model generation steps into a unified workflow. ChemSAR is an online pipeline that implements a complete model-building process. It…

CDK
Web
Desktop

CDK Chemistry Development Kit

Facilitates the implementation of software packages in chemoinformatics. The…

Facilitates the implementation of software packages in chemoinformatics. The CDK is an open-source Java library uses as the basis for other open-source projects. Besides its proven usability in…

Chemalot_knime
Desktop

Chemalot_knime

Permits to generate and maintain command line workflows. Chemalot_knime creates…

Permits to generate and maintain command line workflows. Chemalot_knime creates nodes which are connected with each other via a custom KNIME port type. It provides two converter nodes that convert…

Chemalot
Desktop

Chemalot

Provides a set of command line programs for cheminformatics and structure-based…

Provides a set of command line programs for cheminformatics and structure-based design. Chemalot contains more than 30 sub tools. It can be used to perform basic and complex cheminformatics tasks…

Octopus
Desktop

Octopus

Performs docking simulations of an unlimited number of compounds into a set of…

Performs docking simulations of an unlimited number of compounds into a set of molecular targets. Octopus can carry out geometry refinement using the semi-empirical method PM7. It reduces the number…

CADDSuite
Desktop

CADDSuite

A flexible and open workflow-enabled framework for computer-aided drug design.

A flexible and open workflow-enabled framework for computer-aided drug design.

CVSP
Web

CVSP Chemistry Validation and Standardization Platform

Validates and standardizes chemical structure representations. CVSP uses a set…

Validates and standardizes chemical structure representations. CVSP uses a set of systematic rules to proceed. It assists and encourages the processing of chemical structure files in order to offer…

Sybyl-X
Desktop

Sybyl-X

Performs multi-criteria drug design. Sybyl-X provides a complete drug and…

Performs multi-criteria drug design. Sybyl-X provides a complete drug and molecular design environment with comprehensive tools for molecular modelling. This suite includes small molecule and…

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,…

ODDT
Desktop

ODDT Open Drug Discovery Toolkit

Aims to fulfill the need for comprehensive and open source drug discovery…

Aims to fulfill the need for comprehensive and open source drug discovery software. ODDT was developed as a free and open source tool for both computer aided drug discovery (CADD) developers and…

Click2Drug
Dataset

Click2Drug

Contains a comprehensive list of computer-aided drug design (CADD) software,…

Contains a comprehensive list of computer-aided drug design (CADD) software, databases and web services. Click2Drug classifies tools according to their application field, trying to cover the whole…

RDKit
Desktop

RDKit

Provides tools for cheminformatics, computational chemistry, and predictive…

Provides tools for cheminformatics, computational chemistry, and predictive modeling. RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. RDKit provides…

LiveDesign
Desktop

LiveDesign

Allows the sharing of scientific knowledge. LiveDesign simplifies the analysis…

Allows the sharing of scientific knowledge. LiveDesign simplifies the analysis or exploration of data and helps to the transfer of contents between co-workers. This tool includes a web-based…

Seurat
Desktop

Seurat

Streamlines data access and analysis from a broad mixture of in-house and in…

Streamlines data access and analysis from a broad mixture of in-house and in licensed databases, reports, literature, and computational results by providing a wide array of tools for medicinal…

OpenEye
Desktop

OpenEye

Makes most of its technology available as toolkits programming libraries…

Makes most of its technology available as toolkits programming libraries suitable for custom development. OpenEye software is designed for scientific rigor, as well as speed, scalability and platform…

Open Babel
Desktop

Open Babel

An open source chemistry toolbox. Open Babel is a chemical toolbox designed to…

An open source chemistry toolbox. Open Babel is a chemical toolbox designed to speak the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. It's an open,…

Drugster
Desktop

Drugster

Features a novel workflow that guides the user through each logical step of the…

Features a novel workflow that guides the user through each logical step of the iterative 3D structural optimization setup and drug design process, by providing a seamless interface to all…

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