Manage collections, navigation in the chemical space..., look at SMARTS

 

  • Allostery - Allosteric molecules at Chembl - datasets
  • CLEVER - chemical library editing, visualizing and enumerating resource - tool for database, standalone
  • CVSP - Chemistry Validation and Standardization Platform provides a service to users that would like to validate and standardize their chemical structure records - online
  • UniChem - The tool efficiently produces cross-references between chemical structure identifiers from different databases. Chemistry Validation and Standardization - online
  • SMARTSminer - Discriminative Chemical Patterns: Automatic and Interactive Design - standalone
  • Diversity Geni - Diversity Genie is a small but powerful utility to analyze datasets of small organic molecules. Its features include Calculation and comparison of diversity of chemical sets among others - commercial, standalone, diversity sets
  • ChemDiff - ChemDiff is an Indigo-based utility for finding duplications and visual comparison of two files containing multiple structures. SDF, SMILES, CML, MOLFILE input formats are supported. Normalize molecules, etc.. - standalone
  • ChemCom - A Software Program for Searching and Comparing Chemical Libraries - standalone
  • ChemT - An open-source software for building template-based chemical libraries - standalone
  • iMol EyeMol - Interactively display a set of molecules. Classify, browse and select molecules of interest. - standalone
  • 3DFIT - 3D Fragment Consortium: collection of chemically diverse molecules with a particular focus on fragments that incorporate 3D structure - datasets
  • AlloSite - Allosteric modulators filter - Allosteric modulator rules: for simply deciphering the chemical characteristics of allosteric modulators: (i) MW ≤ 600; (ii) RBN ≤ 6; (iii) 2 ≤ nR ≤ 5; (iv) nRIS = 1 or 2; (v) 3 ≤ SlogP ≤ 7. The allosteric-like rule provides a preliminary filter for the identification of allosteric modulators - online filter
  • PPI-HitProfiler - In silico filter to build a compound collection enriched in PPI inhibitors (CDithem) - standalone
  • ChemoPy - Freely available python package for computational biology and chemoinformatics, compute descriptors - standalone (linux, windows)
  • SMARTSeditor - Look at SMARTS - standalone Mac, linux, windows
  • SMARTSviewer - looking at SMARTS - online
  • SMIfp - The SMILES fingerprint Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules. SMIfp is defined here as a scalar fingerprint describing organic molecules by counting the occurrences of 34 different symbols in their SMILES strings, which creates a 34-dimensional chemical space - online and Java application SMIfp-MAPPLET
  • ChemGPS-NP Web - Navigation in biologically relevant chemical space - online
  • MONA - An interactive tool that has been designed to prepare and visualize large small-molecule datasets - standalone
  • Scaffold Hunter - JAVA-based cross-platform open source tool - standalone
  • cApp - A personal database solution for small-molecule compounds. Includes physico-chemical properties, analysis in relation to adherence to likeness rules as well as recognition of pan-assay interference components and cross-linking (Similarity searches) with identical entries in the PubChem Compound Database or user-provided compound libraries as well as compound clustering based on a MaxMin algorithm (Linux and Windows) - standalone. Linux and Windows
  • Assistant - ScreeningAssistant: Free and open-source desktop software dedicated to store and manage chemical libraries in a local or network-accessible MySQL database, and perform various analysis using simple and advanced chemoinformatics methods (Linux and Windows) - standalone
  • DataWarrior - A very nice free tool for Chemistry Aware Data Visualization and Analysis (openmolecules.org). Numerous features from filtering compounds, to data analysis and computation of descriptors (eg, binned log P, log S, druglikeness score, rotatable bonds...automatic SAR, activity cliff, cluster compounds, find similar compounds...search fragments..look all your compounds, 2D, 3D, see physchem parameters...) (for Mac, Windows and Linux) - standalone
  • FAF-Drugs3 - Online ADMET filtering server (new version of FAF-Drugs2), compound collection preparation. At present uses SDF as input, but can take SMILES for instance via the bank-formatter utility. The outputs can be directly piped into other services - Online
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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira