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Molecule editor software tools | Drug discovery data analysis

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.

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(Bienfait and Ertl 013) JSME: a free molecule editor in JavaScript. J Cheminform.

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Bioclipse
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Provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, ... Bioclipse delivers a stable, scalable integration platform for developers and an intuitive workbench for end users. The tool includes a rewritten editor for chemical structures, a table for multiple molecules that supports gigabyte-sized files, as well as a graphical editor for sequences and alignments. It provides advanced functionality in fields such as cheminformatics, bioinformatics, semantic web, spectrum analysis, drug discovery, safety assessment, and general chemistry education.
SMARTSeditor
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 visualization of patterns is based on the visualization concept of the SMARTSviewer. It supports logic combinations as well as atom environment definitions. The generated pattern is converted into a SMARTS string which can be used in any application where the pattern is needed. SMARTSeditor is part of the AMD tools software bundle.
Smoldyn
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 simulations. It treats other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time. It also includes new algorithms for simulating the diffusion of surface-bound molecules and molecules with excluded volume. Smoldyn has proven to be a useful simulation tool for numerous research projects.
JSME
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 provide access to common editing features and allow creation of large and complex molecules. Further customization of the editor is possible by executing arbitrary defined JavaScript callback functions when the structure in the editor is modified or when the mouse pointer moves over an atom.
CH5M3D
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 developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Installation on a web server is straightforward and does not require any server-side modules or special permissions.
ChemEngine
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 supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The program can obviate to some extent the loss of chemical data while at the same time conserve the memory and storage space required at the journal site.
jsMolEditor
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 its functionality in JavaScript on the client side and was able to work on all common web browsers including Internet Explorer, Firefox, Safari, Opera and Chrome. The JavaScript nature of jsMolEditor also made it able to run in standard web browsers without specific plugins or virtual machines.
PrimaDORAC
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 involved in the construction of small molecule drugs (SMDs) topology and parameter files. This tool allows to recognize molecular topologies and delivers about them. This can help in the process of refining general purpose force fields for molecular dynamics simulations, e.g. by increasing their accuracy augmenting the number of atomic types.
SmilesDrawer
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. This software is composed of two components: a parser module that generates a parse tree with the input SMILES and a SMILES drawer module that converse the parse tree obtained to a 2D-structure drawing. The parser function can be applied in other projects and works also as a standalone tool.
CancerIn
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 chemical analogs screening. This web application provides a user-friendly interface with options to draw a chemical compound using Marvin applet. A standalone version of CancerIN is also available and allows users to scan a vast library of molecules for the screening of potential anticancer molecules.
Gabedit
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, analyzing, converting, and animating molecular systems. It can generate a Povray file for geometry, surfaces, contours, and color-coded planes. This tool is developed to facilitate the production of results from quantum chemistry methods through various computational chemistry software (CCS) and to provide a thorough analysis of these results.
DrugMint
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 the variation in the input file provided by the user: (i) “Draw Structure” were user can sketch molecule of interest, (ii) "Virtual Screening" used for screening a chemical library and (iii) "Analog Design" for generating different analogs of a chemical scaffold via using user defined linkers and R-groups.
Pybel
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. Pybel provides a high-level Python interface to the widely-used OpenBabel C++ toolkit. This combination of a high performance cheminformatics toolkit and an expressive scripting language makes it easy for cheminformaticians to rapidly and efficiently write scripts to manipulate molecular data.
BALL / Biochemical Algorithms Library
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 structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers.
TouchMol4Office
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 cheminformatics and bioinformatics in Office and serves as a comprehensive platform for interfacing with internal and external databases. It is powerful structure search capabilities and advanced informatics for biologics and conjugates such as ADCs (antibody-drug-conjugates).
GAMGI / General Atomistic Modelling Graphic Interface
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) makes Random Close Packing structures, Voronoi and coordination polyhedra for arbitrary structures. It comes with comprehensive atomic data, including ionic radius and isotopic data. It can be useful for the scientific community who needs a graphic interface to build and analyse atomic structures or to study atomic structures and to prepare images for presentations.
MedChem Designer
Provides an innovative molecule drawing features and Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) property predictions. MedChem Designer is a chemical structure drawing program, which is able to handle multiple structures. The software allows to predict several properties, sketch chemical reactions and map the atoms in the reactant to their corresponding atoms in the product and extract chemical structures from displayed images in journal articles, Word documents, PowerPoint slides, web pages, etc.
Vimol
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 to allow an easy manipulation of multiple structures. One of the most powerful features of Vimol is an ability to interactively record your actions. Vimol provides an easy way to make animations of molecular systems. The software allows to count the number of atoms of a particular type, like sodium and potassium ions to calculate the total charge.
MMDS / Mobile Molecular DataSheet
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 structure diagrams, with productivity comparable to desktop-based sketchers. The user experience operates on the datasheet, which is a molecular spreadsheet that holds chemical structures, reactions, text, numbers, etc. The app can be used as a hub for interoperability, and can exchange data with other chemically aware apps, as well as being used to access web services and create graphics suitable for use in manuscripts.
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