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

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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