3D structure generator


  • 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 - standalone - 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...
  • CREST - Automated exploration of the low-energy chemical space with fast quantum chemical methods. CREST is an utility/driver program for the xtb program (semiempirical quantum mechanical (SQM) method which is called extended tight binding (xTB)) - standalone
  • Tautomer - Tautomer generator is a program that generates a set of molecules (tautomers) from a molecular core and number of hydrogen atoms - standalone
  • TANGO - high through-put conformation generation and semiempirical method-based optimization tool for ligand molecules - 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
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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira