Tag: Cheminformatics

ChemmineR 3.44.0 – Cheminformatics Toolkit for R

ChemmineR 3.44.0

:: DESCRIPTION

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

 ChemmineR

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 1;24(15):1733-4. doi: 10.1093/bioinformatics/btn307.
ChemmineR: a compound mining framework for R.
Cao Y, Charisi A, Cheng LC, Jiang T, Girke T.

chemViz2 1.1.0 – Cheminformatics Plugin for Cytoscape

chemViz2 1.1.0

:: DESCRIPTION

UCSF chemViz is a Cytoscape plugin that extends the capabilities of Cytoscape into the domain of cheminformatics. chemViz displays 2D diagrams of compounds specified by InCHI or SMILES strings. chemViz can also calculate Tanimoto similarities of compounds and use the values to create chemical similarity networks. Part of such a network is shown above. The 2D diagrams can be presented as scalable independent windows or as part of a table also showing Cytoscape attributes and calculated compound descriptors, including number of hydrogen bond donors, number of hydrogen bond acceptors, molecular weight, ALogP, molecular refractivity, number of Rule of Five violations, and several more. Any of the calculated descriptors can be mapped onto Cytsocape attributes where they can be used by the VizMapper and saved with the session.

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

chemViz

:: REQUIREMENTS

:: DOWNLOAD

  chemViz

:: MORE INFORMATION

UNICON – Cheminformatics File Conversion

UNICON

:: DESCRIPTION

UNICON is a command-line tool to cope with common cheminformatics tasks. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, and PDB via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states and conformer ensembles.

::DEVELOPER

Computational Molecular Design

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

UNICON 

:: MORE INFORMATION

CDK-Taverna 2.0.5.4 – Workflow Management System for Cheminformatics

CDK-Taverna 2.0.5.4

:: DESCRIPTION

CDK Taverna project based on the “Pipelining Technology” idea tries to address the advantages of software libraries and sophisticated information systems.The project combines two other open-source projects:

The Taverna workbench as a workflow container.
The Chemistry Development Kit (CDK) as a basic chemo-/bioinformatics library.

::DEVELOPER

CDK-Taverna Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

CDK-Taverna

:: MORE INFORMATION

Citation:

Kuhn T, Willighagen EL, Zielesny A, Steinbeck S:
CDK-Taverna: an open workflow environment for cheminformatics.
BMC Bioinformatics 2010, 11:159.