Name | Description | Reference | Web page |
---|---|---|---|
Avogadro | GUI for molecular modelling and computational chemistry | G. Hutchison M. Hanwell | |
cclib | Parse computational chemistry output files | [72] | |
CCP1GUI | GUI for computational chemistry | Jens Thomas | |
ChemAzTech | Manage a chemical laboratory database | Rémy Dernat | |
ChemSpotlight | Chemistry file indexer for MacOSX | G. Hutchison | |
ChemT | GUI for generating combinatorial libraries | Rui Abreu | |
ChemTool | 2D molecular drawing | [73] | |
CMDF | Library for handling and preparing multi-scale multi-paradigm simulations | [74] | |
Confab | Systematically generate conformers | [36] | |
DockoMatic | Automate the preparation and analysis of AutoDock runs | [75] | |
DOVIS 2.0 | Automate the preparation and analysis of AutoDock runs | [76] | |
FAF-Drugs2 | ADMET filtering of molecular datasets | [77] | |
FMiner2 | Large-scale chemical graph mining based on backbone refinement classes | ||
Ghemical | GUI for computational chemistry | Tommi Hassinen | |
Gnome Chemistry Utils | 2D chemical editor, 3D viewer, chemical calculator and periodic table for Linux | Jean Bréfort | |
iBabel | MacOSX interface to Open Babel and other Open chemistry tools | Chris Swain | http://homepage.mac.com/swain/Sites/Macinchem/page65/ibabel3.html |
Kalzium | GUI showing information on the periodic table of the elements | Carsten Niehaus | |
Lazar | Lazy Structure-Activity Relationships for toxicity prediction | [80] | |
Molekel | GUI for computational chemistry | Ugo Varetto | |
molsKetch | 2D chemical editor | Harm van Eersel | |
MyChem | Chemistry extension to the MySQL database | J. Pansanel | |
NanoEngineer-1 | Computer-aided design for the nanoscale | Nanorex, Inc. | |
NanoHive-1 | Simulator for the study, experimentation, and development of nanotech entities | Brian Helfrich | |
OpenMD | Open Source molecular dynamics engine | [81] | |
Open3DQSAR | High-throughput chemometric analysis of molecular interaction fields | ||
OSRA | Extracts chemical structures from images | [84] | |
PgChem | Chemistry extension to the PostgreSQL database | Ernst-Georg Schmidt | |
Pharao | Pharmacophore discovery and searching | Silicos NV | |
Pharmer | Pharmacophore searching | [85] | |
Piramid | Shape-based alignment of molecules | Silicos NV | |
PyADF | Library for handling and preparing quantum mechanical multi-scale simulations | [86] | |
PyRx | GUI for virtual screening with protein-ligand docking | Sargis Dallakyan | |
QMForge | GUI for analysing results of quantum chemistry calculations | [72] | |
RMG | Reaction Mechanism Generator | [87] | |
Sci3D | Interactive visualization of 3D models of scientific data, such as molecular structures and surfaces | T.J. O'Donnell | |
Sieve | Filter molecules from datasets | Silicos NV | |
SMIREP | Generation of fragment-based structure-activity relationships | [88] | |
Stripper | Extract molecular scaffolds | Silicos NV | |
Toxtree | Toxic hazard estimation using decision trees | Ideaconsult Ltd. | |
V_Sim | Visualize atomic structures such as crystals and grain boundaries | Damien Caliste | |
WebBabel | Web application for file format conversion | T.J. O'Donnell | |
XDrawChem | 2D molecular editor | Bryan Herger | |
XtalOpt | Extension to Avogadro for crystal-structure prediction | [89] | |
YASARA | GUI for molecular graphics, modeling and simulation | Elmar Krieger | |
ZODIAC | GUI for molecular modelling and docking | [90] |