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: Bienfait and Ertl, 2013.
Desktop app
ChemEngine ChemEngine

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…

Desktop app
ParmEd ParmEd

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…

Desktop app
MOIL MOIL

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…

Web app
Ketcher Ketcher

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…

Desktop app
Vimol Vimol

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…

Desktop app
ICEDIT ICEDIT

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…

Desktop app
BKChem BKChem

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…

Desktop app
GROMACS GROMACS

GROMACS

Automatically handles wide classes of biomolecules, such as proteins, nucleic…

Automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in.

Web app
Desktop app
Optical Structure… Optical Structure Recognition Application

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,…

Desktop app
Gabedit Gabedit

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,…

Web app
Chemozart Chemozart

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…

CH5M3D CH5M3D

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…

Desktop app
GROningen MOlecular… GROningen MOlecular Simulation

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.

Web app
Learning, Observing… Learning, Observing and Outputting Protein…

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.

Desktop app
Multi-Conformation… Multi-Conformation Continuum Electrostatics

MCCE Multi-Conformation Continuum Electrostatics

A biophysics simulation program combining continuum electrostatics and…

A biophysics simulation program combining continuum electrostatics and molecular mechanics.

Desktop app
NAMD NAMD

NAMD

A parallel molecular dynamics code designed for high-performance simulation of…

A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Desktop app
Abalone Abalone

Abalone

A general purpose molecular modeling program focused on molecular dynamics of…

A general purpose molecular modeling program focused on molecular dynamics of biopolymers.

Web app
3D Crystal Viewer 3D Crystal Viewer

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.

Desktop app
Jmol Jmol

Jmol

An open-source Java viewer for chemical structures in 3D.

An open-source Java viewer for chemical structures in 3D.

Web app
JSDraw JSDraw

JSDraw

Draw and display chemical/biological structures on the Web.

Draw and display chemical/biological structures on the Web.

Web app
JSmol JSmol

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.

Web app
VectorMol VectorMol

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.

Desktop app
ensochemEditor ensochemEditor

ensochemEditor

A universally usable chemical editor for molecules and reactions.

A universally usable chemical editor for molecules and reactions.

Desktop app
JavaGrins JavaGrins

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…

Desktop app
JMolDraw JMolDraw

JMolDraw

2-D chemical structure drawing program.

2-D chemical structure drawing program.

Desktop app
MCDL MCDL

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.

Web app
Molinspiration Molinspiration

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.

Desktop app
Chirys Draw Chirys Draw

Chirys Draw

An innovative application for drawing molecular structures and reactions.

An innovative application for drawing molecular structures and reactions.

Desktop app
VLifeBase VLifeBase

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.

Desktop app
Chemis3D Chemis3D

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.

Web app
ChemWriter ChemWriter

ChemWriter

Chemical structure drawing, display & more in pure JavaScript.

Chemical structure drawing, display & more in pure JavaScript.

Web app
Flash Molecular Editor Flash Molecular Editor

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.

Web app
MolEditor MolEditor

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.

Web app
MolView MolView

MolView

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

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

Desktop app
SketchEl SketchEl

SketchEl

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

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

Desktop app
Accelrys JDraw Accelrys JDraw

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…

Desktop app
Chemtool Chemtool

Chemtool

A small program for drawing chemical structures on Linux and Unix systems.

A small program for drawing chemical structures on Linux and Unix systems.

Desktop app
ChemWindow ChemWindow

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…

Desktop app
ICM Chemist ICM Chemist

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.

Desktop app
Marvin Marvin

Marvin

Intuitive applications and API for chemical sketching, visualization and data…

Intuitive applications and API for chemical sketching, visualization and data exploration.

Desktop app
Spartan Spartan

Spartan

A molecular modeling package for teaching, and learning, chemistry.

A molecular modeling package for teaching, and learning, chemistry.

Desktop app
Avogadro Avogadro

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.

Desktop app
Biochemical… Biochemical Algorithms Library

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…

Desktop app
Bioclipse Bioclipse

Bioclipse

Provides advanced functionality in fields such as cheminformatics,…

Provides advanced functionality in fields such as cheminformatics, bioinformatics, semantic web, spectrum analysis, drug discovery, safety assessment, and general chemistry education.

Desktop app
ChemDoodle ChemDoodle

ChemDoodle

Contains literally thousands of features for working with chemical graphics.

Contains literally thousands of features for working with chemical graphics.

Desktop app
ChemDraw ChemDraw

ChemDraw

Drawing tool for chemists to create publication-ready, scientifically…

Drawing tool for chemists to create publication-ready, scientifically intelligent drawings for use in ELNs, databases and publications and for querying chemical databases.

Desktop app
Elemental Elemental

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.

Desktop app
Ascalaph Ascalaph

Ascalaph

A general purpose molecular modeling software that performs quantum mechanics…

A general purpose molecular modeling software that performs quantum mechanics calculations.

Desktop app
BIOVIA Draw BIOVIA Draw

BIOVIA Draw

Enables scientists to draw and edit complex molecules, chemical reactions and…

Enables scientists to draw and edit complex molecules, chemical reactions and biological sequences with ease, facilitating the collaborative searching, viewing, communicating, and archiving of…

Desktop app
JChemPaint JChemPaint

JChemPaint

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

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

Desktop app
JME JME

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.

Web app
JSME JSME

JSME

A free molecule editor written in JavaScript. JSME was developed as direct…

A free molecule editor written in JavaScript. JSME was developed as direct successor of the popular JME applet, using the JME codebase, therefore although being a new program, it benefits from 15…

Desktop app
XDrawChem XDrawChem

XDrawChem

A drawing application designed for drawing and analyzing chemical structures…

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

Desktop app
ChemSketch ChemSketch

ChemSketch

A drawing package that allows you to draw chemical structures including…

A drawing package that allows you to draw chemical structures including organics, organometallics, polymers, and Markush structures.

Web app
PRODRG PRODRG

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…

Web app
PubChem Sketcher PubChem Sketcher

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.

Desktop app
MedChem Designer MedChem Designer

MedChem Designer

A tool that combines innovative molecule drawing features with ADMET property…

A tool that combines innovative molecule drawing features with ADMET property predictions.

Desktop app
Pybel Pybel

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.…

ChemJuice Deprecated ChemJuice

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.

Web app
Graphical input of… Deprecated Graphical input of SMILES

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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