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3D structure generators for small chemical cmpds


CONFECT Conformations are generated as well as ranked by means of normalized frequency distributions derived from the Cambridge Structural Database (CSD). Following an incremental construction approach, conformations are selected from a systematic enumeration within energetic boundaries. The new tool is benchmarked in several different ways, indicating that it allows the efficient generation of high-quality conformation ensembles. These ensembles are smaller than those produced by state-of-the-art tools, yet they effectively cover conformational space


Warning the 3D structure of cmpds in CSD can be significantly different from the one of the same cmpd co-crystallized in the presence of a macromolecular partners...

Tautomer Tautomer generator is a program that generates a set of molecules (tautomers) from a molecular core and number of hydrogen atoms standalone
Open Babel babel standalone
RDKit Cheminformatics and Machine Learning Software. Can generate 3D structures standalone
COSMOS COSMOS 3D Structure Predictor online
NEWLEAD Computer program for the automatic    generation of candidate structures compound searching - standalone
LSD  Automatic structure elucidation of small organic molecules from 2D NMR data standalone
Acpype A tool based on Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN tools or ARIA standalone
PHENIX  A software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods. It can generate via the modules eLBOW (electronic ligand builder and optimization workbench) proper restraint files standalone
Omega 2D to 3D conversion commercial demo
ICM 2D to 3D conversion commercial demo
SPORES Structure PrOtonation and REcognition System standalone
AMBER Reduce from AmberTools can add hydrogens... standalone
Chemaxon 2D to 3D conversion commercial or free
XDrawChem Possible 2D to 3D conversion with BUILD3D standalone
Cyndi The pre-compiled version of Cyndi (Windows), parameter input file, Tripos force field parameter file and the test set of 329 high-resolution and drug-concerned small molecules determined from X-ray structures in mol2 format standalone
TINKER  Molecular modeling software standalone
PRODRG2  Server 2D to 3D (one can find geometry-restraint files) online
Grade The Grade Server: the Global Phasing restraint dictionary generator online
EasyMol A Java tool standalone
VeraChem 2d to 3d online
Confab  A command-line application to systematically generate diverse low-energy conformers for molecules standalone
Balloon  2d to 3d structure generator standalone
VEGA ZZ 2d to 3d can be found online
MolEdit  Web server for 2D molecular editor & 3D structure optimization online
X-ray structure Crystallography Open Database database
NMRShiftDB  Free collection, some molecules are in 3D database
FROG2 2d to 3d and more online
DG-AMMOS  2d to 3d online and standalone, see also AMMOS to minimize molecules once docked into a binding site
ChemoPy Freely available python package for computational biology and chemoinformatics standalone (linux, windows)
MolEdit 2d to 3d online
Probuilder Peptide builder online
dataset to test ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers. The tool was developped using about 660 PDB files with ligands to test the 3D structure generator. The list of PDB files is in the Supplement of J Chem Inf Modeling (J. Chem. Inf. Model., 2010, 50 (4), pp 534–546) datasets
ALFA It is a fast computational tool for the conformational analysis of small molecules that uses a custom-made iterative algorithm to provide a set of representative conformers in an attempt to reproduce the diversity of states in which small molecules can exist, either isolated in solution or bound to a target. ALFA is distributed free of charge upon request from the authors (see Klett J et al., J Chem Inf Modeling 2014) standalone