Skip to main content
Try Wikispaces Classroom now.
Brand new from Wikispaces.
Pages and Files
Free and open source resources
Mining chemical information
Structural analysis of diverse sets using scaffold analysis .
Assignment 1.2 Aliaksandr Krukau
Assignment 1.2 EduH
Assignment 6 Aliaksandr Krukau
I571_Fall 2015 Edu Harguindey
Toxicophores in a Malarial Bioassay
Add "All Pages"
Free and open source resources
Programming / statistical environments and pipelining
- statistical computing package including clustering and predictive modeling. Has been extended for cheminformatics with
- statistical computing and workflow package extended for cheminformatics / QSAR with
- pipelining / workflow and visualization tool for cheminformatics
- Chemistry Development Kit - Java toolkit for cheminformatics
- Open Source Chemistry Tookbox (see
- chemistry cartridge for Oracle that uses the CDK (see
Visualization and navigation
- network visualization and analysis tool - extended for cheminformatics by
Gephi is an interactive visualization and exploration platformfor all kinds of networks and complex systems, dynamic and hierarchical graphs.
GraphInsight is a visualization software that lets you explore graph data through high quality interactive representations.
Weave(web based data Visualization)
Weave (BETA 1.0) is a new web-based visualization platform designed to enable visualization of any available data by anyone for any purpose. Weave is an application development platform supporting multiple levels of user proficiency – novice to advanced – as well as the ability to integrate, disseminate and visualize data at “nested” levels of geography.
Processing is an open source programming language and environment for people who want to create images, animations, and interactions. Initially developed to serve as a software sketchbook and to teach fundamentals of computer programming within a visual context, Processing also has evolved into a tool for generating finished professional work.
D3.js is a small,
: Software for multivariate data visualization
The Databionic ESOM Tools is a suite of programs to perform data mining tasks like clustering, visualization, and classification with
Emergent Self-Organizing Maps
(ESOM). Features include:
UNM Biocomputing tools
including bioactivity data mining, clustering, depiction, format conversion, drug-likeness and many more tools
- Molecular property (including LogP) and activity prediction
- converting relational database to RDF
- OWL editor
- XML, JSON visualization
Semantic Web Development Tools
Semantic Web tools on semanticweb.org
Sixty four free chemistry database
listed in Depth First (covered pretty much all the public database), highlight some of them:
PubChem- definitely the biggest one, as Jan 2011, PubChem includes 31 million entries.
Chemspider- covers over 26 million structures as Nov 2011, high quality data and with many detailed properties
ChEBI- focuses on the ontology of chemical compounds
DrugBank- Drug resources
ZINC - commercial compounds for virtual screening, contains over 13 million
“eMolecules discovers sources of chemical data by searching the Internet, and receives submissions from data providers such as chemical suppliers and academic research institutions.”
KEGG: it is not free now
Other resource lists
OSDD list of computational resources
Chemical Information Sources Wiki
Archive of chemistry softwares
help on how to format text
Turn off "Getting Started"