Chemical Library Enumeration. Chemical Library Enumeration (This workflow can be found on the KNIME Workflow Public Server under 050_Applications/050001_ChemicalLibraryEnumeration Note that this workflow requires the installation of various nodes from the community update site!)
The Workflow The workflow demonstrates how a chemist could create a virtual library of Amides based on a set of Acids and Amines.For the enumerated products, some molecular properties are then calculated and the products are filtered based on the Lipinski "rule of 5". In order to demonstrate the interoperability of the different community contributions, the workflow uses nodes from the RDKit, CDK, and Indigo integration. In practice, this is, of course, not absolutely necessary. The Report The workflow uses a QuickForm to allow the user to select the type of plot to accompany a report combining numeric, text and image data along with the selected graph in a summarized report: Sharing Metanodes. Molinspiration WebME Editor. ChEMBLdb. Online Chemical Modeling Environment. Online Chemical Modeling Tutorials. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information.
To create a new QSAR model in OCHEM the user must prepare the training and (optional) validation sets, configure the preprocessing of molecules (standardization and 3D optimization), choose and configure the molecular descriptors and the machine learning method, select the validation protocol (N-fold cross-validation or bagging) and, when the model has been calculated, review the predictive statistics and save or discard the model.
The following sections describe each of the aforementioned steps in detail. Training and validation sets, machine learning method and validation Training and validation datasets. One of the most important steps in model development is the preparation of input data, i.e., a training set that contains experimentally measured values of the predicted property. Chemistry Freeware.
On this page I post reviews and links to freeware chemistry programs available for download at other sites around the internet.
All of the programs are ones that I have used, or currently use. None-the-less, I take no responsiblity for any problems you might experience as a result of installing any of these applications. Unless otherwise noted, the programs are for Windows systems. ACD/ChemSketch 12 Freeware. ACD continues to release updates to the outstanding Chemsketch freeware. Accelrys Draw is a program that allows you to generate structural formulas for complex molecules using a very intuitive drag-and-drop interface. No-fee Accelrys JDraw for academic and non-commercial use. Discovery Studio Visualizer 4. ChemAxon produces a wide range of Java-based chemistry tools, and they offer free academic licenses (you must register with them). Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. EniG. Virtual Laboratory Software.
LogP Calculator. NCI/CADD Group Chemoinformatics Tools and User Services. The PubChem Project. PubChem Download Page. This file contains the structures downloaded from the PubChem FTP site that have at least one assay result associated with them that was obtained in the context of the NIH Common Fund (previously: NIH Roadmap) Molecular Libraries Probe Production Centers Network (previously: Molecular Libraries Screening Center Network), part of the Common Fund’s Molecular Libraries and Imaging program .
It is organized by unique chemical structures (“Compounds” in PubChem parlance), i.e. assay results for possibly multiple different samples (“Substances” in PubChem parlance) have been combined into the one record representing the unique chemical structure. Placeholder assays (assays containing a single record only) have been filtered out. Explanation of the property data fields in the SD file (note - properties present in the original PubChem files have been copied unchanged, for the explanation of those properties we point directly to the appropriate PubChem document ):
PubChem Download Service. 2,4,6-tri-tert-butylphenol - PubChem Public Chemical Database. NCBI: PubChem DB download. ASN.1 Format Summary An International Standards Organization (ISO) data representation format used to achieve interoperability between platforms.
For data specifications and conversion tools, see NCBI Data Specification below. BLAST Microbial Genomes Performs a BLAST search for similar sequences from selected complete eukaryotic and prokaryotic genomes. BLAST RefSeqGene. CHMIS-C. Practical chem. Chemical Databases - WWW Chemistry Guide. ChemMine. Chemical Search Engine. ACToR. ChemSpider - Database of Chemical Structures and Property Predictions.
SDF File Extension - Open .SDF files. PowerMV Molecular Viewer. PowerMV: A software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search.
Jack Liu, Jun Feng, Atina Brooks and Stan Young National Institute of Statistical Sciences Basic Functions: • Supports MDL SDF format • Displays molecules in multiple columns. • Displays properties contained in SD file in a table. • Anti-alias technology for best picture quality. • Table of molecule pictures and properties can be exported to Excel (Office XP and above) to generate personalized reports. • Calculates three types of binary atom pair descriptors and continuous weighed burden numbers. . • Searches over ACL library to determine possible mechanisms or side effects. BASIC VERSION Download Now! Version 0.61 released! Notes: Users from Denmark and some other European countries should change Regional Setting to U.S. to avoid a file saving bug. AFFILIATE VERSION Download (requires affiliate userid and password) Version 0.71 released! Main Page - Avogadro - Free cross-platform molecule editor.