Cheminfostream

MyMol - an Open Source Web-based molecular database

Matteo Floris, University of Padova, presented on the Cheminformatics Hub on the development of MyMol, an Open-source Web-based molecular database.  MyMol is based on PHP and Mysql and also makes use of the JME molecular editor from Peter Ertl (Novartis) for structure entry and molecular file generation.  Rule of 5 searching over structures is carried out using Supersmiles coding, which is used for the automatic generation of molecular descriptors.

In order to further improve and develop MyMol, Matteo Floris is seeking collaboration with other Open Source Developers.

Barry Hardy
www.douglasconnect.com

 

Chemical Informatics & Modelling Open Source Community

I would like to support a free-access Chemical Informatics & Modelling Open
Source Community area on the Cheminformatics Hub where discussions
between researchers and developers on Open Source projects, proposals and
collaborations could take place.  Supporting facilities provided will
include collaborative document sharing, discussion, alerting, and chat
and  voice-based meeting facilities.  For such an area to work and be
active, we need a core working group who would be willing to "drive" and
actively participate in this community.  If interested in joining such a
group, please contact me with your interest and suggestions.

Optimised Virtual Screening

Drug research is often termed as searching for a needle in a haystack. Virtual screening is widely recognised as a valuable tool to effectively reduce the size of the 'haystack' by about one order of magnitude. In the presentation of Miklos Vargyas, Chemaxon on the Cheminformatics & Modelling Hub, he discusses in detail techniques that can further improve the efficiency of the virtual screening procedure.

Dr. Vargyas’s recent work  has focused on topological pharmacophore similarity based search where only a set of known active 2D structures is known. The pharmacophores of these structures are analysed by perceiving the pharmacophoric characteristic of each individual atom. Pharmacophore patterns are transformed into a topological cross-correlation histogram. These correlation histograms are molecular descriptors that represent the pharmacophoric character of structures in a mathematically tractable form. Proximities (metrics) like the Euclidean distance and the Tanimoto coefficient are applied to estimate the dissimilarity between two such descriptors.

Deploying Grid Computing for Generating Drug Candidates

Karl Harrison, Oxford University reports in a Virtual Talk on the Cheminformatics and Modelling site on the drug research they have carried out using a Grid computing approach on a massive scale. This Oxford University/UD.com Project has covered three areas: anti-cancer drug discovery, anthrax poison cures, and recently investigating smallpox virus enzymes.  The Project has been able to harness 300,000 years of computing time as a result of PC computing cycles donated by more than 2 million project members.   With such a massive donation the project was effectively deploying a distributed calculation engine that was faster than the world’s fastest current supercomputer. (continued...)

eCheminformatics Virtual Conference and Poster Session

All eCheminformatics Virtual Conference lectures with audio are now available on the Cheminformatics Hub at http://echeminfo.com/

The eCheminformatics international virtual conference is held on the Internet and brings together researchers to discuss the applications of Cheminformatics methods to Drug Discovery. 

The conference consists of Internet-based Virtual Lectures accompanied by audio. Discussions can take place on the Web site using both asynchronous and synchronous discussion-based mechanisms. Recordings of the presentations are now viewable in the Conference Library and will continue to be available in 2004. 

Poster Session

All conference Hub registrants have the opportunity to present a conference Poster on a cheminformatics subject. Posters can be presented in Word, pdf, html or Powerpoint format.  If you or a colleague wish to present a Poster at the conference, please submit your abstract to us with Title, author(s), institution, contact email address, contact phone number and abstract of no more than 300 words.  Registrants will subsequently be able to directly upload their poster to the Poster Session area of the Hub.

Speaker Presentations

You can view the eCheminformatics 2003 Speaker program with Abstracts at the following link:

http://echeminfo.colayer.net/html/speakerinformation.htm

Barry Hardy
www.douglasconnect.com

About the Cheminformatics & Modelling Community of Practice

The Cheminformatics & Modelling website echeminfo.com is an Internet-based community system for the cheminformatics and chemistry communities which was opened in November 2003.  Activities include:

- Virtual Conferences and Lectures: keep up with the latest developments from experts around the globe, talk to presenters live or listen to recorded events, ask your questions
- Networking:  contact other members on the Hub for advice, recruitment or potential collaboration
- Company Exhibitor area:  view latest product information and news from companies which supply cheminformatics products and services, alert them with your questions or arrange an online meeting with them
- Meetings facilities:  Hub members may use the Hub meeting facilities to arrange a private or open meeting with other Hub members
- Library:  View previous presentations, lectures and panel discussions on the Hub. 
- Community and Discussion groups:  create your own sub-community and discussion group where you can carry out your own group discussions

Please visit echeminfo.com and register to access facilities and to be kept informed of upcoming activities.

Barry Hardy
www.douglasconnect.com

Cheminfostream opens

I have started this Cheminfostream Blog as a place where I will post news and views in the areas of cheminformatics, chemical modelling and chemical information.  The Blog is a complementary if somewhat different different space to our recently launched Cheminformatics & Modelling Community of Practice Hub at eCheminfo.com.  In this Blog I will report on presentations, discussions and activities occuring on this Hub but will also be including selected news and developments from other sources and projects and the field in general.  I welcome your comments and interaction!

Barry Hardy
www.douglasconnect.com