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Molecule editor tools

A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system.Source text:(Bienfait and Ertl 013) JSME: a free molecule editor in…
SMARTSeditor
Desktop

SMARTSeditor

Supports editing of given SMARTS or editing of chemical pattern without…

Supports editing of given SMARTS or editing of chemical pattern without knowledge of the SMARTS language from scratch. The SMARTSeditor is a graphic editing tool for generic chemical patterns. The…

DataWarrior
Desktop

DataWarrior

Combines dynamic graphical views and interactive row filtering with chemical…

Combines dynamic graphical views and interactive row filtering with chemical intelligence. DataWarrior is a universal data analysis and visualization program, whose embedded cheminformatics…

Smoldyn
Desktop

Smoldyn

Simulates each molecule of interest individually to capture natural…

Simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. Smoldyn is a computer program for cell-scale biochemical…

GROMACS
Desktop

GROMACS

Performs molecular dynamics simulations and energy minimization. GROMACS…

Performs molecular dynamics simulations and energy minimization. GROMACS provides a rich set of calculation types, preparation and analysis tools. It also distributes computational work across…

Bioclipse
Desktop

Bioclipse

Provides 2D-editing, 3D-visualization, file format conversion, calculation of…

Provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, ... Bioclipse delivers a stable, scalable integration platform for developers and an intuitive…

MOIL
Desktop

MOIL

A package to perform a variety of biomolecular calculations and simulations…

A package to perform a variety of biomolecular calculations and simulations using molecular mechanic force fields. MOIL contains unique features such reaction path calculations, simulations of long…

OSRA
Web
Desktop

OSRA Optical Structure Recognition Application

An optical structure recognition application based on modern advances in image…

An optical structure recognition application based on modern advances in image processing implemented in open source tools. OSRA can read documents in over 90 graphical formats including GIF, JPEG,…

NAMD
Desktop

NAMD

Enables molecular dynamics simulations of biomolecular systems. NAMD has been…

Enables molecular dynamics simulations of biomolecular systems. NAMD has been designed to permit continuous software development in view of ever-changing technologies, to utilize parallel computers…

ChemEngine
Desktop

ChemEngine

Harvests 3D molecular data from the supporting information of scientific…

Harvests 3D molecular data from the supporting information of scientific research articles that are normally available from publisher’s resources. ChemEngine recognizes textual patterns from the…

MolPrime
Mobile

MolPrime

Provides the powerful drawing capabilities of the Mobile Molecular DataSheet in…

Provides the powerful drawing capabilities of the Mobile Molecular DataSheet in a smaller and more accessible application. MolPrime is a lightweight app that combines structure drawing capabilities…

SAR Table
Mobile

SAR Table

Provides a convenient way to produce tables of structures and activity or…

Provides a convenient way to produce tables of structures and activity or property data, by providing scaffolds, substituents, and data. SAR Table is an application for iOS devices which operates on…

Jamberoo
Desktop

Jamberoo

Displays, analyzes, edits, converts, and animates molecular systems. Jamberoo…

Displays, analyzes, edits, converts, and animates molecular systems. Jamberoo is a program in constant development to improve the existing code and to add new functionality. This application is a…

NOC
Desktop

NOC

Uses as an easy-to-use protein explorer for structure visualization, analysis.…

Uses as an easy-to-use protein explorer for structure visualization, analysis. NOC is a powerful software for crystallographic mapping, modelling and refinement and an efficient viewer for…

ParmEd
Desktop

ParmEd

Facilitates creating and easily manipulating molecular systems that are fully…

Facilitates creating and easily manipulating molecular systems that are fully described by a common classical force field. ParmEd is capable of reading and writing to a wide array of different file…

Chemozart
Web

Chemozart

A 3D Molecule editor and visualizer built on top of native web components.…

A 3D Molecule editor and visualizer built on top of native web components. Chemozart offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web…

Abalone
Desktop

Abalone

Allows macromolecular simulations. Abalone is a general purpose molecular…

Allows macromolecular simulations. Abalone is a general purpose molecular modeling program which focuses molecular dynamics modeling of biopolymers. The software supports methods such as Replica…

Jmol
Desktop
Web

Jmol

Allows to visualize three-dimensional (3D) chemical structures. Jmol is a…

Allows to visualize three-dimensional (3D) chemical structures. Jmol is a standalone viewer which provides features for molecules, crystals, materials, and biomolecules.

Ketcher
Web

Ketcher

A molecule editor for the input and the editing of chemical molecules. Ketcher…

A molecule editor for the input and the editing of chemical molecules. Ketcher incorporates high performance, good portability and light weight. Ketcher supports the standalone mode in which no…

Molinspiration
Web
Desktop

Molinspiration

Allows creation and editing of molecules in browsers without Java support and…

Allows creation and editing of molecules in browsers without Java support and without any plugins.

Chemtool
Desktop

Chemtool

Permits to draw chemical structures. Chemtool is a small program offers…

Permits to draw chemical structures. Chemtool is a small program offers essentially unlimited undo/redo, two text fonts plus symbols, seven colors, drawing at several zoom scales, and square and…

ICEDIT
Desktop

ICEDIT

A windows software that allows users to drawing of chemical structures,…

A windows software that allows users to drawing of chemical structures, reactions and fragments. ICEDIT supports standard query features. It provides additional chemical features like full superatom…

Ascalaph
Desktop

Ascalaph

Performs quantum mechanics calculations for initial molecular model…

Performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics simulations in the gas or in condensed phase. Ascalaph is a general purpose molecular…

BKChem
Desktop

BKChem

A free chemical drawing program. BKChem allows users to quickly draw molecules…

A free chemical drawing program. BKChem allows users to quickly draw molecules through basic functions on the GUI and advanced functionalities such as sprout drawing, and default/user-defined…

JSME
Web
Desktop

JSME

Supports drawing and editing of molecules and reactions. JSME is a molecule…

Supports drawing and editing of molecules and reactions. JSME is a molecule editor developed as direct successor of the JME applet. The built-in substituent menu and several keyboard shortcuts…

Atomdroid
Mobile

Atomdroid

Includes molecular viewer/builder capabilities with integrated routines for…

Includes molecular viewer/builder capabilities with integrated routines for geometry optimizations. Atomdroid provides means of computational chemistry, namely Monte Carlo simulations and local…

Gabedit
Desktop

Gabedit

A freeware graphical user interface that offers preprocessing and…

A freeware graphical user interface that offers preprocessing and postprocessing adapted (to date) to nine computational chemistry software packages. Gabedit includes tools for editing, displaying,…

GROMOS
Desktop

GROMOS GROningen MOlecular Simulation

It has been developed for the dynamical modelling of (bio)molecules using the…

It has been developed for the dynamical modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization.

MCCE
Desktop

MCCE Multi-Conformation Continuum Electrostatics

A biophysics simulation program combining continuum electrostatics and…

A biophysics simulation program combining continuum electrostatics and molecular mechanics.

Pybel
Desktop

Pybel

Provides convenience functions and classes that make it simpler to use the Open…

Provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python, especially for file input/output and for accessing the attributes of atoms and molecules.…

BALL
Desktop

BALL Biochemical Algorithms Library

A comprehensive rapid application development framework for structural…

A comprehensive rapid application development framework for structural bioinformatics. BALL provides an extensive C++ class library of data structures and algorithms for molecular modeling and…

KegDraw
Desktop

KegDraw

Draws chemical compound structures and glycan structures with capabilities to…

Draws chemical compound structures and glycan structures with capabilities to search against the KEGG databases. KegDraw is a Java application.

Green Lab…
Mobile

Green Lab Notebook

Allows recording of multistep chemical reactions, using molecular structure,…

Allows recording of multistep chemical reactions, using molecular structure, name and stoichiometry as the primary components. The Green Lab Notebook is a structure-centric tool for capturing…

MMDS
Mobile

MMDS Mobile Molecular DataSheet

Implements core chemical structure technology and delivers it in the form of a…

Implements core chemical structure technology and delivers it in the form of a powerful app that runs on all phone and tablet form factors. MMDS provides the ability to draw presentation quality 2D…

TouchMol
Desktop

TouchMol

Helps chemists to draw, share and search chemical and biological structures.…

Helps chemists to draw, share and search chemical and biological structures. TouchMol is a set of add-ins to Microsoft Office applications including Excel, Word, PowerPoint and OneNote. It enables…

jsMolEditor
Desktop

jsMolEditor

Mades a significant difference from other editors available on web pages.…

Mades a significant difference from other editors available on web pages. jsMolEditor is a JavaScript based molecule editor that works completely independently on the client side. It implements all…

Chemkit
Desktop

Chemkit

Uses as a library for chemistry applications, particularly in the areas of…

Uses as a library for chemistry applications, particularly in the areas of chem-informatics, molecular visualization and molecular modeling. Chemkit is an open source software written in C++ using…

DCE ChemPad
Mobile

DCE ChemPad

Allows users to draw chemical structures and calculate molecular weight,…

Allows users to draw chemical structures and calculate molecular weight, molecular formula and to send the molfile. DCE ChemPad shows the capabilities of the Dendro Chemical Editor control for…

MolPad
Mobile

MolPad

Allows you to draw chemical structures freehand with a finger, stylus or mouse,…

Allows you to draw chemical structures freehand with a finger, stylus or mouse, just as you would with pencil and paper. MolPad is a chemical structure drawing app specifically designed for tablets.…

Chem4SharePoint
Desktop

Chem4SharePoint

Enable Chem-Bioinformatics in Microsoft SharePoint. Chem4SharePoint is a…

Enable Chem-Bioinformatics in Microsoft SharePoint. Chem4SharePoint is a software that draw or import chemical structures and biologics, display chemical structures and biologics and search chemical…

SMole
Desktop

SMole

Permits to analyze a molecular structure by rotating, moving and zooming it.…

Permits to analyze a molecular structure by rotating, moving and zooming it. The SMole is an application that can view, edit and build molecules in 2D/3D.

IMoleDraw
Mobile

IMoleDraw IMolecular Draw

Permits to analyze a molecular structure by rotating, moving and zooming it.…

Permits to analyze a molecular structure by rotating, moving and zooming it. The IMoleDraw is an application that can view, edit and build molecules in 2D.

Chem4D
Desktop

Chem4D Chemistry 4-D Draw

Creates multi-line graphs of different styles. It supports non-linear and…

Creates multi-line graphs of different styles. It supports non-linear and linear curve fitting, response curve fitting and data analysis Chemistry 4-D Draw is a next-generation chemistry program…

PLT
Desktop

PLT

Produces chemical drawings and outputting them in a variety of formats. PLT is…

Produces chemical drawings and outputting them in a variety of formats. PLT is a program that provides routines for producing all rings and line types used in chemical structures, formatted text…

iMolview
Mobile

iMolview

Allows to browse protein, DNA, and drug molecules in 3D. iMolview makes a…

Allows to browse protein, DNA, and drug molecules in 3D. iMolview makes a direct link to the Protein Data Bank (PDB) and DrugBank. The user can interact with the 3D structures by touching the…

CH5M3D
Desktop

CH5M3D

A library written in JavaScript to allow for the simple creation of web-based…

A library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in…

LOOPP
Web

LOOPP Learning, Observing and Outputting Protein Patterns

A fold recognition program based on the collection of numerous signals, merging…

A fold recognition program based on the collection of numerous signals, merging them into a single score, and generating atomic coordinates based on an alignment into a homologue template structure.

3D Crystal…
Web

3D Crystal Viewer

A simple and free atomic (crystalline or molecular) structure model viewer.

A simple and free atomic (crystalline or molecular) structure model viewer.

JSDraw
Web

JSDraw

Draw and display chemical/biological structures on the Web.

Draw and display chemical/biological structures on the Web.

JSmol
Web

JSmol

It is the extension of the Java-based molecular visualization applet Jmol as an…

It is the extension of the Java-based molecular visualization applet Jmol as an HTML5 JavaScript-only web app.

VectorMol
Web

VectorMol

Enables to draw molecules within most web browsers without noticeable loading…

Enables to draw molecules within most web browsers without noticeable loading time or local installation.

ensochemEditor
Desktop

ensochemEditor

A universally usable chemical editor for molecules and reactions.

A universally usable chemical editor for molecules and reactions.

JavaGrins
Desktop

JavaGrins

A Java based chemical editor that derives SMILES equivalents of sketched…

A Java based chemical editor that derives SMILES equivalents of sketched molecules and reactions and vice versa. With JavaGrins one can draw a molecule or reaction and obtain its canonical SMILES…

JMolDraw
Desktop

JMolDraw

A two dimensional (2D) chemical structure drawing program.

A two dimensional (2D) chemical structure drawing program.

MCDL
Desktop

MCDL

A small Java molecular viewer/editor for chemical structures, stored in Modular…

A small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation.

Chirys Draw
Desktop

Chirys Draw

An innovative application for drawing molecular structures and reactions.

An innovative application for drawing molecular structures and reactions.

VLifeBase
Desktop

VLifeBase

Provides features to build a molecule from scratch using 2D Draw and a single…

Provides features to build a molecule from scratch using 2D Draw and a single click conversion to 3D.

Chemis3D
Desktop

Chemis3D

A Java Applet which renders virtual 3D molecular models within a Web document.

A Java Applet which renders virtual 3D molecular models within a Web document.

ChemWriter
Web

ChemWriter

Chemical structure drawing, display & more in pure JavaScript.

Chemical structure drawing, display & more in pure JavaScript.

FlaME
Web

FlaME Flash Molecular Editor

A molecular structure editor (molecule editing tool) for web pages, based on…

A molecular structure editor (molecule editing tool) for web pages, based on Flash technology and related methods (JavaScript functions) is presented.

MolEditor
Web

MolEditor

A free software to create, edit and export a simple chemical database online.

A free software to create, edit and export a simple chemical database online.

MolView
Web

MolView

A web application for drawing, searching and viewing chemical structures.

A web application for drawing, searching and viewing chemical structures.

SketchEl
Desktop

SketchEl

An interactive chemical molecule sketching tool, and molecular spreadsheet data…

An interactive chemical molecule sketching tool, and molecular spreadsheet data entry application.

Accelrys JDraw
Desktop

Accelrys JDraw

Gives application developers a lightweight, no-fee structure editor for the…

Gives application developers a lightweight, no-fee structure editor for the development of custom web and rich client applications that require chemical structure queries and/or chemical structure…

ChemWindow
Desktop

ChemWindow

A software tool for chemical structure drawing and publishing worldwide. Now…

A software tool for chemical structure drawing and publishing worldwide. Now with integrated solutions to modify, store, search, and retrieve chemical structures and properties, ChemWindow offers…

ICM Chemist
Desktop

ICM Chemist

A standalone suite of programs for chemical drawing and editing, chemical…

A standalone suite of programs for chemical drawing and editing, chemical database generation, chemical searching, clustering, and enumeration.

Marvin
Desktop

Marvin

Models linkage disequilibrium (LD) using a simple multivariate Gaussian…

Models linkage disequilibrium (LD) using a simple multivariate Gaussian distribution. MarViN is an algorithm that can improve genotyping at variants seen in the reference panel. The key feature of…

Spartan
Desktop

Spartan

Provides molecular modeling package for teaching and learning chemistry.…

Provides molecular modeling package for teaching and learning chemistry. Spartan offers a full range of computational models, spanning Molecular Mechanics, Semi-Empirical models, Hartree-Fock…

Vimol
Desktop

Vimol

A molecular viewer and editor. Vimol was inspired by the vi text editor and…

A molecular viewer and editor. Vimol was inspired by the vi text editor and bears many similarities with it. It allows creation of new bindings or modification of existing ones. This tool is designed…

Avogadro
Desktop

Avogadro

An advanced molecule editor and visualizer designed for cross-platform use in…

An advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

ChemDoodle
Desktop

ChemDoodle

Contains literally thousands of features for working with chemical graphics.

Contains literally thousands of features for working with chemical graphics.

ChemDraw
Desktop

ChemDraw

Offers a streamlined and simplified set of products to satisfy the requirements…

Offers a streamlined and simplified set of products to satisfy the requirements of researchers, students and faculty involved in chemistry and related subjects. ChemDraw is a suite of drawing…

Elemental
Desktop
Mobile

Elemental

A comprehensive set of chemical structure editors that enable scientists to…

A comprehensive set of chemical structure editors that enable scientists to draw, edit and save structures and reactions as well as calculate properties.

BIOVIA Draw
Desktop

BIOVIA Draw

Enables to draw and edit complex biologics, molecules and chemical reactions.…

Enables to draw and edit complex biologics, molecules and chemical reactions. BIOVIA Draw provides structure and query drawing, allows to register, search and report on chemically modified peptide or…

JChemPaint
Desktop

JChemPaint

Chemical 2D structure editor application/applet based on the Chemistry…

Chemical 2D structure editor application/applet based on the Chemistry Development Kit.

MedChem…
Desktop

MedChem Designer

Provides an innovative molecule drawing features and Absorption, Distribution,…

Provides an innovative molecule drawing features and Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) property predictions. MedChem Designer is a chemical structure drawing…

XDrawChem
Desktop

XDrawChem

A drawing application designed for drawing and analyzing chemical structures…

A drawing application designed for drawing and analyzing chemical structures and reactions.

ChemSketch
Desktop

ChemSketch

Allows to draw chemical structures such as organics, organometallics, polymers,…

Allows to draw chemical structures such as organics, organometallics, polymers, and Markush structures. ChemSketch permits to calculate molecular properties, clean and view 2D and 3D structure, name…

PRODRG
Web

PRODRG

It will take a description of a small molecule and from it generate a variety…

It will take a description of a small molecule and from it generate a variety of topologies for use with GROMACS, WHAT IF, Autodock, HEX, CNS, REFMAC5, SHELX, O and other programs, as well as…

PubChem…
Web

PubChem Sketcher

A Web-based drawing tool for interactive sketching of chemical query structures.

A Web-based drawing tool for interactive sketching of chemical query structures.

ChemJuice
Mobile

ChemJuice

A mobile app to create a database of molecules. It can also calculate molecular…

A mobile app to create a database of molecules. It can also calculate molecular weight, formula and percent composition by element and can email the structure wherever you wish.

JME
Desktop

JME

A Java applet which allows to draw/edit molecules and reactions (including…

A Java applet which allows to draw/edit molecules and reactions (including generation of substructure queries) and to depict molecules directly within an HTML page.

GRINS
Web

GRINS Graphical input of SMILES

A molecular editor which works exclusively via the HTML protocol.

A molecular editor which works exclusively via the HTML protocol.

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