Molecule editor
A molecule editor is a computer program for creating and modifying representations of chemical structures.
Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, via 2D computer graphics or 3D computer graphics, respectively. Two-dimensional output is used as illustrations or to query chemical databases. Three-dimensional output is used to build molecular models, usually as part of molecular modelling software packages.
Database molecular editors such as Leatherface,[1] RECAP,[2] and Molecule Slicer[3] allow large numbers of molecules to be modified automatically according to rules such as 'deprotonate carboxylic acids' or 'break exocyclic bonds' that can be specified by a user.
Molecule editors typically support reading and writing at least one file format or line notation. Examples of each include Molfile and simplified molecular input line entry specification (SMILES), respectively.
Files generated by molecule editors can be displayed by molecular graphics tools.
Standalone programs
[edit]2D structure editing
[edit]| Program | Developer(s) | License | Platforms | Info |
|---|---|---|---|---|
| ACD/ChemSketch | ACD/Labs | Proprietary | Windows | A chemically intelligent drawing interface allowing creation of 2D structures for organics, organometallics, polymers, and Markush structures. Freeware version available. |
| Biovia Draw | MDL Information Systems | Proprietary | Windows | Formerly ISIS/Draw, now owned by Dassault Systèmes. Focuses on 2D chemical structure editing.[4] |
| ChemDraw | PerkinElmer | Proprietary | Windows, macOS | Primarily for editing 2D chemical structures and reactions |
| JChemPaint | JChemPaint Developers | GNU LGPL | Cross-platform | A 2D structural formula editor written in Java |
| ChemWindow | Wiley | Proprietary | Windows | Freeware for academic research and teaching; part of the KnowItAll software environment |
| XDrawChem | XDrawChem Developers | GNU GPL | Windows, macOS, Linux | A 2D chemical structure drawing tool based on OpenBabel |
| MarvinSketch | Chemaxon | Proprietary | Cross-platform | Comprehensive chemical editor for drawing, querying, and displaying chemical structures |
| MolView | Herman Bergwerf | Copyright | Browser-based | Lightweight 2D chemical editor with 3D visualizer integrated with external databases like PubChem |
3D structure editing
[edit]| Program | Developer(s) | License | Platforms | Info | Last Release |
|---|---|---|---|---|---|
| Avogadro | Avogadro project team | GNU GPL | Windows, macOS, Linux | A 3D molecule editor and visualizer. | 10 February 2024 
|
| BALLView | BALL project team | GNU GPL | Windows, macOS, Linux | 3D molecular modeling, visualization, and editing tool. | |
| Gabedit | Abdulrahman Allouche | BSD | Windows, macOS, Linux | A 3D molecule editor with visualization capabilities. | 27 July 2021
|
| Ascalaph Designer | Agile Molecule | GNU GPL | Windows, Linux | A freeware 3D molecule editor. | 2009 |
| MOE | Chemical Computing Group | Proprietary | Windows, macOS, Linux | Includes 3D molecular sketching, editing, and 2D to 3D conversion. | June 2024 |
| SAMSON | Inria | Proprietary | Windows, macOS, Linux | A modular platform for computational nanoscience, including 3D molecular editing. | 2024 |
| Spartan | Wavefunction, Inc. | Proprietary | Windows, macOS, Linux | Focused on 3D molecular modeling and simulation. | 14 May 2024 |
| Amira (software) | Visage Imaging Zuse Institute Berlin |
Proprietary | Windows, macOS, Linux | Includes 3D visualization tools. Trial version available. | |
| Deneb | AtelGraphics | Proprietary | Windows, Linux | GUI for simulation packages, including 3D editing. | |
| PyMOL | Schrödinger | Proprietary (Open-source version available) | Cross-platform | Popular molecular visualization tool with basic 3D editing capabilities for structural analysis. | 9 April 2024
|
| ChimeraX | UCSF | Proprietary Free for academic use | Windows, macOS, Linux | A molecular graphics tool for visualization, analysis, and basic 3D modeling. | 13 June 2024
|
| IQmol | Andrew Gilbert | Open source | Cross-platform | A molecular editor with visualization capabilities, designed to work with Q-Chem. | 10 October 2024
|
| VMD | University of Illinois | Free for non-commercial use | Cross-platform | 3D Molecular visualization tool that includes structure editing through the Molefacture plugin. | 30 November 2016
|
| HyperChem | Hypercube, Inc. | Proprietary | Windows, Linux | A 3D molecular modeling tool with quantum chemistry and molecular dynamics features. Discontinued. | 29 November 2011
|
| Chemcraft | Chemcraft developers | Proprietary | Windows, Linux | Visualization and analysis tool for quantum chemistry and molecular structures. | 28 September 2024
|
| YASARA | YASARA Biosciences | Proprietary (Free version available) | Cross-platform | Molecular graphics and modeling software focused on structural biology, with extensive 3D capabilities. | 5 October 2024
|
| Biovia Discovery Studio | Dassault Systèmes | Proprietary | Windows, Linux | Advanced molecular modeling platform with features for 3D visualization, simulations, and drug discovery. | 2024
|
| Biovia Materials Studio | Dassault Systèmes | Proprietary | Windows, Linux | A 3D editing and visualization tool specifically designed for materials science applications. | 2024
|
| CrystalMaker | CrystalMaker Software Ltd | Proprietary | Windows, macOS | Designed for building, visualizing, and analyzing crystal structures in 3D. | 11 July 2024
|
| Py-ChemShell | CSE Collaboration | LGPL3 | Linux, Windows | A 3D editor for preparing quantum mechanical and molecular mechanics calculations. | 12 December 2023
|
| Molecular Constructor | Alexander Teplukhin | Freeware | Windows, macOS, Linux, Android, iOS | A free 3D molecular builder and editor with geometry optimization features. | 26 February 2016
|
| WebMO | WebMO LLC | Proprietary (Free version available) | Browser-based | A web-based interface for computational chemistry packages with integrated 3D molecular editor. | 2024
|
| Miew | EPAM Systems | MIT License | Browser-based | A 3D molecular viewer and editor designed for visualization and editing of large molecular complexes. | 26 August 2024
|
Java Applets
[edit]| Applet | Developer(s) | License | Info |
|---|---|---|---|
| JChemPaint | GNU LGPL | Editor and viewer applets | |
| JME Molecule Editor | Peter Ertl | Proprietary | freeware available from Molinspiration; Freeware for noncommercial use |
JavaScript embeddable editors
[edit]| Program | Developer | License | Desktop Browser IE6-7-8 | Desktop Browser other | iPad | iPhone | Android | Info |
|---|---|---|---|---|---|---|---|---|
| Kekulé Program | Kekule.js Lab | MIT License | Yes | Yes | Unknown | Unknown | Unknown | |
| Ketcher | EPAM Systems | Apache License | Unknown | Yes | Unknown | Unknown | Unknown | Originally developed by GGA Software Services before being bought by EPAM Systems |
See also
[edit]Notes and references
[edit]- ^ Kenny, Peter W.; Sadowski, Jens (2005). "Structure Modification in Chemical Databases". Chemoinformatics in Drug Discovery. Methods and Principles in Medicinal Chemistry. pp. 271–285. doi:10.1002/3527603743.ch11. ISBN 9783527307531.
- ^ Lewell, Xiao Qing; Judd, Duncan B.; Watson, Stephen P.; Hann, Michael M. (1998). "RECAP-Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry". Journal of Chemical Information and Computer Sciences. 38 (3): 511–522. doi:10.1021/ci970429i. PMID 9611787.
- ^ Vieth, Michal; Siegel, Miles G.; Higgs, Richard E.; Watson, Ian A.; Robertson, Daniel H.; Savin, Kenneth A.; Durst, Gregory L.; Hipskind, Philip A. (2004). "Characteristic Physical Properties and Structural Fragments of Marketed Oral Drugs". Journal of Medicinal Chemistry. 47 (1): 224–232. doi:10.1021/jm030267j. PMID 14695836.
- ^ "Biovia Draw datasheet" (PDF). Dassault Systemes. Retrieved 2023-04-25.