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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…

PrimaDORAC
Web

PrimaDORAC

Allows to work on the assignment of partial charges, chemical topology and…

Allows to work on the assignment of partial charges, chemical topology and bonded parameters in organic molecules. PrimaDORAC is intended to do automatically and reliably most of the tedious work…

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…

EGFRpred
Web

EGFRpred

Predicts inhibitors of mutant form of Epidermal Growth Factor Receptor (EGFR).…

Predicts inhibitors of mutant form of Epidermal Growth Factor Receptor (EGFR). EGFRpred provides a web server and a standalone package. Users only needs to submit a scaffold structure along with the…

CancerIn
Web
Desktop

CancerIn

Predicts anticancer potency of an unknown molecule and its GI50 across…

Predicts anticancer potency of an unknown molecule and its GI50 across different cancer cell lines. CancerIN is a web server that consists of three modules for designing, library screening and…

SmilesDrawer
Desktop

SmilesDrawer

Draws molecular structures from simplified molecular-input line-entry system…

Draws molecular structures from simplified molecular-input line-entry system (SMILES) strings client-side. SmilesDrawer can exploit web applications for the visualization of molecular structures.…

ChemAgora
Dataset

ChemAgora

Gives access to a collection of chemical properties and their related links.…

Gives access to a collection of chemical properties and their related links. ChemAgora compiles sets available through the OECD eChemPortal coupled to a selection of public repositories dealing with…

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…

libefp
Desktop

libefp

Consists in a Message Passing Interface/OpenMP (MPI/OpenMP) parallelization of…

Consists in a Message Passing Interface/OpenMP (MPI/OpenMP) parallelization of the Effective Fragment Potential (EFP) method. libefp permits efficient utilization of multiple computer nodes and…

DrugMint
Web

DrugMint

Predicts drug-likelihood of a compound. DrugMint is a predictive model that…

Predicts drug-likelihood of a compound. DrugMint is a predictive model that allows users to interactively draw/modify a molecule using a Marvin applet. It incorporates different modules to support…

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…

pyEFP
Desktop

pyEFP

Permits users to feign large polyatomic molecules and polymers, at the same…

Permits users to feign large polyatomic molecules and polymers, at the same time reducing coordinates of all fragments to the same inner structure. pyEFP is based on the Effective Fragment Potential…

The Decider
Web

The Decider

Allows users to select density functional and basis set combinations. The…

Allows users to select density functional and basis set combinations. The Decider is a web application that is based on game theory coupled with existing benchmark data. It is composed of two mains…

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…

Tinker
Desktop

Tinker

Provides functions for molecular mechanics and dynamics, with some features for…

Provides functions for molecular mechanics and dynamics, with some features for biopolymers. Tinker employs an implementation of atomic multipole-based electrostatics with explicit dipole…

SeeSAR
Desktop

SeeSAR

Allows users to work on visual compound prioritization as well as compound…

Allows users to work on visual compound prioritization as well as compound evolution.

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…

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.

Chirys Draw
Desktop

Chirys Draw

Provides a downloadable molecular spreadsheet. Chirys Draw is an application…

Provides a downloadable molecular spreadsheet. Chirys Draw is an application for drawing molecular structures and reactions. This resource takes advantage of multi-touch capabilities to make drawing…

MolView
Web

MolView

Permits to draw, search and view chemical structures. MolView is an…

Permits to draw, search and view chemical structures. MolView is an open-source, intuitive web-application to make chemistry and biology. This application consists of two main parts, a structural…

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…

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…

PubChem…
Web

PubChem Sketcher

Allows users to automatically sketch chemical structures. PubChem Sketcher is a…

Allows users to automatically sketch chemical structures. PubChem Sketcher is a web-based drawing which consists, at its core, in a CACTVS cheminformatics toolkit application script. The software…

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…

ghemical
Desktop

ghemical

Computes energy and gradient using quantum mechanical methods and molecular…

Computes energy and gradient using quantum mechanical methods and molecular mechanics methods. ghemical is a computational chemistry package that provides options for studying a molecular system…

Garlic
Desktop

Garlic

Identifies transmembrane segments. Garlic is an open source molecular…

Identifies transmembrane segments. Garlic is an open source molecular visualization program designed for visualization and analysis of membrane proteins. It visualizes any type of molecules and…

GAMGI
Desktop

GAMGI General Atomistic Modelling Graphic Interface

Constructs, views and analyses atomic structures. GAMGI is an atomistic…

Constructs, views and analyses atomic structures. GAMGI is an atomistic application that (i) determines any point group of symmetry, (ii) builds crystals for any space group of symmetry, and (iii)…

coord_util
Desktop

coord_util

Reads and writes geometries in several common formats. coord_util is a library…

Reads and writes geometries in several common formats. coord_util is a library for reading, manipulating and writing molecule geometries. This package includes reader modules for several coordinate…

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…

TouchMol4Office
Desktop

TouchMol4Office

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…

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