Cheminfostream

eCheminfo Virtual Community Activities in Cheminformatics

When I started the eCheminfo community of practice in late 2003 we focused initially on using the approach of virtual conferencing and communications to get the community started.  More recently I have given more attention to developing face-to-face conference and workshop activity and initiating collaborative research. While on this journey it has been personally rewarding to have met and made contact with hundreds of scientists in the international community and to additionally be involved in supporting their networking, career development and research in drug design, discovery and modelling. It has also been rewarding to have just met so many great people and to have had the chance to interact with them, be it on a computer, in a workshop exercise, or on a punt trying to get down the river as we usually do when we are in Oxford.  So far we seem to be better on computer-based physics than boat physics!

And so I have come full circle and can see the need to prioritise the virtual community aspects of eCheminfo further again, to support the continuation of all these worthwhile interactions in the community.  So LinkedIn is one place to start.  I have been on there for some years and we have had a group area, but have not really done much with it.  It has primarily been useful for some introductions between people.  However recent feature additions for discussion, posting of news, job announcements etc. have been added, so it seems worthwhile to try using it more for supporting continuing interactions in the community.  So I am initiating today invitations to the eCheminfo community to join us there for discussion, news and networking on what is happening in the world of drug discovery informatics, cheminformatics, bioinformatics, etc.  Use of the group is intended for scientific and professional exchange purposes only.  As included in our mission we encourage cross-disciplinary cross-sector participation so from medicinal chemists in the pharmaceutical industry through toxicologists in government institutes through PhD students working on their modelling research problems are welcome!

To request joining the eCheminfo LinkedIn group please follow the following link and introduce yourself with a group joining request:

https://www.linkedin.com/e/gis/1173/77EB680070FF/

I also really welcome suggestions from the community there on what you would like to see as further developments in coming years!

Barry

Cheminformatics Workshop Week on Drug Discovery in Oxford

We are running the eCheminfo drug discovery workshop week at Oxford University this year the week of 20-24 July.

Workshop groups will study problems with hands-on examples using computational drug discovery methods and discuss issues highlighted by examples and Case Studies presented by instructors. A Case Study set with a focus on Kinases will be used to link all workshop activities throughout the week.

Workshop topics will include:

- Virtual Screening
- Structure-based Drug Design & Planning
- Ligand Optimisation & Library Design
- Structure Search, Similarity and Property Estimation
- Bioactive Conformations & Conformational Search
- Pharmacophore Modelling for Lead Identification
- Fragment-based Drug Design
- Free Energy-based Calculation of Binding Energies
- Modelling Reactions & Synthetic Feasibility of Workshop Libraries
- Application of ADME and Metabolic Property Prediction to Library Design

A Bursary Award will be used to support the attendance of a selection of academic participants, who may be working in any area of research related to drug discovery. To apply for the bursary please send an email with a) description of your research (ca. 500 words); b) your training needs (ca. 500 words), c) your CV to eCheminfo -[at]- douglasconnect.com by 27 February 2009.

More information on program can be found at: eCheminfo Drug Discovery Workshop 2009 in Oxford Program

Registration: Registration for eCheminfo Drug Discovery Workshop 2009 in Oxford

or contact Nicki Douglas at eCheminfo -(at)- douglasconnect.com

Predictive ADME and Toxicology workshop in Oxford

For the first time we are holding a predictive ADME and Toxicology workshop in Oxford this summer.  It should be a valuable and rewarding experience that adds to our summer workshop activities there.  I believe we have a really good group of facilitators gathered that should make for an excellent working week. We will take a working, problem-solving approach to case study datasets throughout the week.

Here is the program as a pdf download:

Download ECheminfoADMETProgramOxford09

More detail on the program abstracts and schedule in the continuation below.

Barry

Program & Schedule for eCheminfo 08 Oxford Workshop Week

The program, abstracts and schedule for the 5 Day eCheminfo Hands-on Drug Discovery Workshop Week (21-25 July 2008) at the Medical Sciences Teaching Center, Oxford University, Oxford, UK is provided below. (follow continuation)

More Information is available at http://www.echeminfo.com/COMTY_training

To complete registration arrangements for the workshop, please contact Nicki.Douglas –(at)- douglasconnect.com, +41 61 851 0461

Drug Discovery Workshop Week in Oxford

The 5 Day eCheminfo Hands-on Drug Discovery Workshop Week will take place this year 21-25 July 2008 at the Medical Sciences Teaching Center, Oxford University, Oxford, UK.

Topics to be covered include Virtual Screening & Docking; Structure-based Drug Design; Ligand Optimisation & Library Design; Structure Search, Similarity and Property Estimation; Data Mining, Analysis & Visualisation; Pharmacophore Modelling for Lead Identification; Fragment-based Drug Design; QSAR-based Predictive Toxicology; and Quantitative Spectrometric Data-Activity Relationship Modelling.

These workshops are aimed to provide a set of stimulating workshops using latest advanced modelling techniques of relevance to chemists, life scientists and modellers working in drug discovery. The workshop group studies problems with hands-on examples using leading-edge software and discusses complex issues highlighted by examples and case studies presented by instructors. A variety of leading drug discovery software packages and an IT classroom are used by instructors and participants to work through problems.

More Information is available at http://www.echeminfo.com/COMTY_training

Download Program as a pdf:

Download eChemProgramOxford08-v1.2.PDF

To register for the workshop, please contact Nicki.Douglas –(at)- douglasconnect.com, +41 61 851 0461

Barry Hardy

eCheminfo Community of Practice Manager

eCheminfo cheminformatics chemoinformatics bioinformatics Medicinal Chemistry Computational Chemistry Virtual Screening Docking Molecular Modelling Molecular Modeling pharmaceutical pharma meeting workshop training Oxford Critical Path toxicology Bursary Life Sciences Pharma Drug DiscoveryResearch and Development Drug Development Healthcare Innovation Knowledge Management events

Drug Discovery Workshop, Oxford, September 10-14

I am pleased to announce that we will be holding the hands-on eCheminfo
Drug Discovery Workshop week a second time this year in Oxford the week
of 10-14 September. First option on places will go to the waiting list from
the June workshop but there nevertheless still are additional places available.
If interested in attending, please see links below for further information:

Latest Advances in Drug Discovery Design & Planning Methods
a Hands-on 5 Day eCheminfo Advanced Training Workshop Week

25-29 June 2007 (registration closed) AND 10-14 September 2007

Chemistry Research Laboratory, Oxford University, Oxford, UK

Brochure: http://www.douglasconnect.com/files/eChemProgramOxford07-Sept-v1web.PDF
Abstracts and Bios on Website: http://echeminfo.colayer.net/COMTY_training
Photos from Class of 2006: http://www.echeminfo.com/COMTY_oxfordphotos06
Feedback from Class of 2006: http://www.echeminfo.com/COMTY_oxfordfeedback06

Bursary Award for Drug Discovery Training Week in Oxford

The 5 Day eCheminfo Advanced Drug Discovery Training Week will take place 25-29 June 2007 at the Chemistry Research Laboratory, Oxford University, Oxford, UK. Topics to be covered include Virtual Screening & Docking, Structure-based Drug Design, Library Design, Latest advances in ADME & Predictive Toxicology, Data Mining, Analysis & Visualisation, Pharmacophores, Pharmacokinetics & Pharmacodynamics, Physiological-based Simulation and Integration of Cheminformatics & Bioinformatics Tools & Data.

These workshops are aimed to provide a set of stimulating workshops using latest advanced modelling techniques of relevance to chemists, life scientists and modellers working in drug discovery. The workshop group studies problems with hands-on examples using leading-edge software and discusses complex issues highlighted by examples and case studies presented by instructors. A variety of leading software packages and an IT classroom are used by instructors and participants to work through challenging problems.

A Bursary Award sponsored by Chemical Computing Group (CCG) will be used to support the attendance of one academic participant, who may be working in any area of chemistry related to drug discovery. To apply for the bursary please send an email with a) description of your research; your training needs (ca. 500 words each), b) your CV to echeminfo [at] douglasconnect.com by 28 February. The recipient of the award will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of the training on their research progress and will be notified by 15 March. We gratefully acknowledge the sponsorship support of CCG.

Download Program Brochure (pdf):

Download eChemProgramOxford07-v3web.PDF

More Information is available at http://www.echeminfo.com/COMTY_training

Barry Hardy

eCheminfo Community of Practice Manager

eCheminfo cheminformatics chemoinformatics bioinformatics Medicinal Chemistry Computational Chemistry Virtual Screening Docking Molecular Modelling Molecular Modeling pharmaceutical pharma meeting workshop training Oxford Critical Path toxicology Bursary Life Sciences Pharma Drug DiscoveryResearch and Development Drug Development Healthcare Innovation Knowledge Management events

eCheminfo Membership & Workshop Activity for 2007

During November I will be planning the 2007 programs for the eCheminfo Advanced Training Week in Oxford and the InterAction Meeting in Bryn Mawr.  Please contact me with your interests and proposals!

Latest Advances in Drug Discovery Design & Planning Methods
a Hands-on 5 Day eCheminfo Advanced Training Workshop Week
June 25-29, Chemical Research Laboratory, Oxford University, Oxford, UK

Latest Advances in Drug Discovery & Development
eCheminfo Community of Practice InterAction Meeting
15-18 October 2007, Bryn Mawr College, Philadelphia, PA, USA
Themes: Screening, Medicinal Chemistry, Drug Design, Toxicology, Structural Biology, Bioinformatics, Cheminformatics

eCheminfo Gold membership
This entitles members to access eCheminfo meeting proceedings including audio, access to our Executive Insights reports from meeting and community of practice activities, and additional member discounts on meeting and training registration fees. 

Download eCheminfo2007MembershipForm.pdf

Barry Hardy

eCheminfo cheminformatics chemoinformatics bioinformatics Medicinal Chemistry Computational Chemistry Virtual Screening Docking Molecular Modelling Molecular Modeling pharmaceutical pharma meeting workshop conference management Bryn Mawr Philadelphia Critical Path toxicology personalised medicine Life Sciences Pharma Drug DiscoveryResearch and Development Drug Development Healthcare Innovation Knowledge Management events

Co-led Knowledge Management Training

As apparent from our discussions at Bryn Mawr College last week at the eCheminfo and InnovationWell meetings, knowledge management (KM) stands to play a key role in emerging new practices to drug discovery and development, healthcare and new services in personalised medicine.  However there is need to improve our understanding of and competency in KM and its emerging best practices to achieve breakthroughs such as innovation success in discovery, product development and improving confidence in safety.

A full five-day Certified Knowledge Manager (CKM) workshop will be held in Basel, 27 November – 1 December 2006.  The training will be jointly led for the first time by Swiss faculty who bring their own extensive experience of knowledge management and European practice to enrich the quality of the learning program.

The workshop week will be co-led by Douglas Weidner, President, International Knowledge Management Institute; Pavel Kraus, Founding Partner of aht'intermediation GmbH & President, Swiss Knowledge Management Forum; Beat Knechtli, Director and Chief Knowledge Officer, PwC Switzerland, and Barry Hardy, Director, KM Institute Switzerland

Case Studies & Discussions will be used to illustrate the application of KM principles and best practices.

More information is available at:
http://barryhardy.blogs.com/theferryman/2006/10/swiss_faculty_c.html

Barry Hardy

KM Institute KM Institute Switzerland meeting workshop training management executive CKM KM Knowledge Management Knowledge Management Training Management Training Basel Innovation Switzerland events

In silico Library Enumeration of Synthetically Feasible Libraries

Virtual synthesis programs are not yet widely used by synthetic chemists and many may doubt that such approaches can match the skills of the experienced chemist.  Nevertheless ChemAxon have created a Java-based Reactor system to process reactions according to rules captured in the syntax of the Chemical Terms language for reactivity, selectivity, and side reaction exclusion.  Using such a system, discovery enumeration is significantly extended beyond a desired product library to create instead a reaction library, which has taken into account availability of starting compounds, experimental conditions, and prior available chemistry reaction knowledge on reaction types and their chemo-, regio-, and stereoselectivity issues.  A combinatorial synthesis library of a million such reactions can currently be built using several hours of CPU.

Oxford-based Inhibox, founded by Graham Richards, chairman of Chemistry at the University of Oxford, and headed by CEO Paul Finn, who pioneered the implementation of virtual screening methodologies for Pfizer at Sandwich, have been developing novel computational discovery methods and created Scopius, a very large database of chemical structures for drug discovery. Inhibox are using ChemAxon’s Reactor software to establish optimum conditions to give 'synthetically accessible' libraries with favourable properties for their research, and to create a reaction service, with workflows to create de novo libraries for client projects. “The core functionality to enumerate focused de novo type libraries in Oracle for a number of organic transformations is already available”, according to lead developer Dan Butler at Inhibox who continued “In a nutshell what we are attempting to do with Reactor is create a service which will primarily allow creation of focused de novo approach libraries and secondarily, exhaustive sets, for organic transformations that have (a) a reasonable set of suitable reactants in our commercial database and thus a tangible starting point and (b) are well defined reactions in the literature. In addition the Chemical Terms functionality of Reactor may help us create more accurate product sets. Overall this is quite a large undertaking in many respects, not least of which are the amount of organic transformations available to implement!”

Dan Butler will be joined in Oxford by ChemAxon’s CTO and virtual synthesis expert György Pirok to reveal the results of this work for the first time at the eCheminfo Drug Discovery Training Week at Oxford University (3-7 July 2006). Attendees to their workshop will be able to use provided software to create virtual reaction libraries and to work with the workshop leaders to establish optimum conditions to give 'synthetically accessible' libraries with favourable properties for their research. Dr. Pirok commented that “Currently we are developing a GUI so that synthetic chemists, who are not familiar with programming or command line tools, will be able to generate these reaction libraries. This GUI also contains an editor for modifying existing reactions or creating new ones. Workshop participants in Oxford will be one of the first set of users trying the new desktop Reactor application and GUI, and will get to try the newest features not previously released.  We will try to create new selective reactions and libraries together during the workshop, that will be of relevance to participants’ interests.”

Barry Hardy
eCheminfo Community of Practice

Training eCheminfo meeting workshop conference management chemistry Life Sciences Pharma Drug Discovery Drug Design Synthetic Chemistry Organic Chemistry Virtual Synthesis Innovation Informatics cheminformatics chemoinformatics IT Molecular Modeling Molecular Modelling events