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

eCheminfo 2009 Drug Discovery meeting at Bryn Mawr - call for contributions

We will hold our fifth annual eCheminfo community of practice meeting on drug discovery informatics at Bryn Mawr College, Philadelphia 13 -16 October 2009.

We invite contributed papers from members of academic, government research and commercial organizations on areas of new research and innovation involving drug discovery research informatics. The work presented should involve innovative new method development or application to drug discovery problems and involving methods from computational chemistry, computational biology, cheminformatics or bioinformatics. Studies including experimental work in medicinal chemistry, screening, in vitro assay development, pre-clinical evaluation, lead optimisation and translational medicine are welcome.

Abstracts for talks (300-500 words) should be submitted to echeminfo -[at]- douglasconnect.com by 31 March 2009, and be accompanied by a short biography of the presenting author (300-500 words). Abstracts approved by the scientific organizing committee will be selected for scheduling on the conference program. Authors will be notified of acceptance as soon as a review of submitted materials takes place and at the latest by 15 April 2009. Abstracts for posters will continue be accepted for review through 31 August 2009.

The following sessions are currently planned:

Pre-conference Workshop on Drug Binding Affinities
chaired by Scott Brown (Abbott Laboratories) and Judith Lalonde (Bryn Mawr College)

Structure-Based Drug Design: The Roles of Conformation, Water and Hydrogen Bonds
chaired by Alan Cheng (Amgen)

Macromolecular Interactions and Networks
chaired by Emil Alexov (Clemson University)

Structure-Based Drug Design: Advanced Scoring Methods
chaired by Natasja Brooijmans (Wyeth)

Data Analysis and Visualisation Applications in Chemical Biology
chaired by Brian Marsden (Structural Genomics Consortium Oxford)

PDB Ligands
chaired by John Westbrook (Rutgers University)

Predictive Toxicology
chaired by Vladimir Poirikov (Russian Academy of Medical Sciences) and Richard Judson (US EPA)

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

Advances in Drug Discovery Informatics

The eCheminfo Autumn Community of Practice Meeting will take place 14-17 October 2008 at Bryn Mawr College, Bryn Mawr, Philadelphia, USA to discuss the latest advances in drug discovery informatics including the following topics:

Cheminformatics, Bioinformatics, Medicinal Chemistry, Drug Discovery Innovation, Structure-based Drug Design, Screening, Docking, Structural Biology, Predictive Toxicology, Predictive ADME, Chemogenomics

Program Summary
Docking & Scoring, chaired by Chaya Duraiswami (GlaxoSmithKline)
Application of MM-PBSA Free Energy Methods in Drug Discovery, chaired by Judith Lalonde (Bryn Mawr College)
Accurate Calculation of pKas, chaired by Paul Labute (Chemical Computing Group)
In Silico-based Chemogenomics, chaired by Fabrice Moriaud (MEDIT)
PDB Ligands: Analysing their Structure & Binding Data, chaired by Marc Nicklaus (National Institutes of Health)
Predictive ADME, chaired by Anthony E. Klon (Pharmacopeia Drug Discovery)
Predictive Toxicology, chaired by Artem Cherkasov (University of British Columbia)

Pre-Conference Workshop, 13 October 2008
Best Practices Virtual Screening Workshop chaired by Barry Hardy (Douglas Connect)

Speakers
John Irwin (UCSF), Georgia McGaughey (Merck), Johannes H. Voigt (Schering Plough), Lance Westerhoff (Quantum Bio), Zsolt Zsoldos (SimBioSys), Alexey Ornufriev  (Virginia Tech), David Case (Rutgers University), Rommie Amaro (USCD), Peter Coveney (Univ. College London), Anna Kohlmann (Ariad Pharmaceuticals), Scott Brown (Abbott), Emil Alexov (Clemson University), Jens Erik Nielsen (University College Dublin, Ireland), Darren Flower (Jenner Institute, UK), Maja Mihajlovic (City College of New York), Michael Keiser (UCSF), Brian Marsden (University of Oxford, UK), Alex Tropsha (UNC), John Westbrook (Rutgers), Howard J Feldman (CCG), Igor V. Filippov (NCI), Raul Cachau (ATP, SAIC-Frederick), Vincent T. Moy (University of Miami), Paul Hawkins (OpenEye), Yulia Borodina (NCBI), Gerhard Wolber (Inte:Ligand, Austria), Marc Nicklaus (NCI), James P. Snyder (Emory), Anne Chaka (NIST), Esther Kellenberger (Univ. Strasbourg, France), Renxiao Wang (SIOC, Shanghai, PR China), Jim Dunbar (University of Michigan), Janna Wehrle (NIGMS), Anton Hopfinger (University of New Mexico), Heidi Einolf (Novartis), Yojiro Sakiyama (Pfizer), Olga Obrezanova (BioFocus DPI, UK), Anthony E. Klon (Pharmacopeia), Artem Cherkasov (University of British Columbia, Canada), Ann Richards (US EPA), Curt Breneman (RPI), Barry Hardy (Douglas Connect), Weida Tong (FDA)

CFP
We invite contributed papers from members of academic, government research and commercial organizations on areas of new research and innovation involving drug discovery research informatics. The work presented should involve innovative new method development or application to drug discovery problems and involving methods from computational chemistry, computational biology, cheminformatics or bioinformatics. Studies including experimental work in medicinal chemistry, screening, experimental toxicology, pre-clinical evaluation, lead optimisation and translational medicine are welcome.

Abstracts (300-500 words) should be submitted to echeminfo -[at]- douglasconnect.com by 31 July 2008, and be accompanied by a short biography of the presenting author (300-500 words). Abstracts approved by the scientific organizing committee will be selected for scheduling on the conference program and in meeting poster sessions. Authors will be notified of acceptance as soon as a review of submitted materials takes place and at the latest by 15 August 2008.

Bursary
Bursary Awards will be used to support the attendance of a selection of academic young investigators at the meeting and workshops. Applicants can be working in any area of research related to drug discovery at the postdoctoral, graduate student and senior undergraduate levels.

To apply for the bursary please send an email with a) your abstract and biography (300-500 words each), b) your CV of 1-2 pages, c) a short description of your interests and career motivations related to drug discovery (300-500 words) to echeminfo -[at]- douglasconnect.com by 31 July 2008. The recipients of the bursary awards will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of attendance at the meeting on their research and career progress. Authors will be notified of acceptance by 15 August 2008.

Poster Session
All InterAction Meeting registrants are eligible to present a Conference Poster. The Poster Sessions will take place in the evenings in Thomas Great Hall on campus, where refreshments and dinner are also served. Poster Abstracts (300-500 words) with Title, Institution, Authors and Contact Information should be submitted to barry.hardy -[at]-
douglasconnect.com  Abstracts will be considered based on date of submission and quality, and will be reviewed and accepted as they are received. To be considered for the formal program, they should be submitted at the very latest by 31 August 2008.

Download Program Brochure (pdf):

Download eChemProgramBrynMawr08-Final-v3.pdf

Contact:
Program: Dr. Barry Hardy, eCheminfo Community of Practice, Douglas Connect. Tel: +41 61 851 0170. barry.hardy -[at]- douglasconnect.com

Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. echeminfo -[at]- douglasconnect.com or go to:

http://echeminfoBM810.eventsbot.com

eCheminfo cheminformatics chemoinformatics bioinformatics Medicinal Chemistry Computational Chemistry Docking pKas Virtual Screening PDB Ligands PDB Chemogenomics ADME ADMET Free Energy Predictive Toxicology Docking Molecular Modelling Molecular Modeling pharmaceutical pharma meeting conference workshop Bryn Mawr Critical Path toxicology Bursary Life Sciences Pharma Innovative Medicines Drug Discovery Research and Development Drug Development Healthcare Innovation Knowledge Management events

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

Bursary Award for Drug Discovery Training 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.

A Bursary Award sponsored by Tripos will be used to support the attendance of one academic participant, 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 15 April 2008. 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 30 April. We gratefully acknowledge the sponsorship support of Tripos.

More information on the workshop program 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

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

Fragment-based Drug Discovery

Fragment-based drug discovery (FBDD) is a rapidly emerging field to identifying novel, small molecule, preclinical development candidates. Because traditional high-throughput screening has had its challenges, due to the complexity and relatively large size of the compounds routinely being screened, FBDD had been gaining momentum as an alternative approach. It starts with very small, low molecular weight, drug fragments which have the potential to keep the overall complexity and molecular weight of each drug candidate low. Traditional bioassays are not able to detect small drug fragments because of their low potency binding to the protein target. Thus, FBDD integrates biophysical techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, isothermal calorimetry with fragment library design and a range of computational methodologies for an efficient hit-to-lead process. The ultimate success of any drug discovery program is measured by the quality and quantity of the drugs it produces. FBDD has been practical in the past decade only, thus too soon to put its stamp yet on marketed drugs. However, we have faith that it will indeed deliver on its promise.

On 17 October 2007 we will hold an eCheminfo Community of Practice conference session at Bryn Mawr College, Philadelphia to discuss latest advances in fragment-based drug discovery. The session will be chaired by Maria Kontoyianni and includes a knowledgeable panel of speakers and discussion leaders: Chaohong Sun (Abbott), Renate Sekul (Graffinity), Woody Sherman (Schrodinger), Georgia McGaughey (Merck) and Stephen Burley (SGX Pharmaceuticals). A description of the session with presentation abstracts follows:

Fragment-based Drug Discovery
http://echeminfo.com/COMTY_conferencesprog07fragment

(Please follow continuation to read abstracts)

eCheminfo Autumn Community of Practice meeting 2007

The eCheminfo Autumn Community of Practice meeting will take place the week of October 15 at Bryn Mawr College, Philadelphia to discuss latest research applications, methods and best practices in drug discovery informatics, design and modelling.

The following conference sessions will be held:
16 October: Virtual Screening, chaired by Christopher Austin (NIH) and Ajay Jain (UCSF)
16 October: Structural Biology, chaired by Max Cummings (Tibotec Pharmaceuticals)
17 October: Structure-based Drug Design, chaired by Jose Duca (Schering-Plough)
17 October: Fragment-based Drug Discovery, chaired by Maria Kontoyianni (Crystax Pharmaceuticals)
18-19 October: Predictive ADME/Toxicology, chaired by Tony Hopfinger (University of New Mexico College of Pharmacy)

Additional workshop activity on virtual screening best practices, knowledge management in R&D and advances in predictive ADME and toxicology will also be held.

Conference speakers include:
Stephen Burley (SGX Pharmaceuticals), Georgia McGaughey (Merck), Charles Lesburg (Schering-Plough), Rick Beger (FDA), Marc Nicklaus (NIH), Woody Sherman (Schrodinger), Daniel Cheney (Bristol Myers Squibb), Paul Labute (Chemical Computing Group), Ajay Jain (UCSF), Alan Cheng (Amgen), Tony Hopfinger (University of New Mexico), Anthony Klon (Pharmacopeia Drug Discovery), Artem Cherkasov (University of British Columbia), Dennis Pelletier (Pfizer), Chaohong Sun (Abbott), Xavier Barril (University of Barcelona), Jose Duca (Schering-Plough), Terry Stouch (JCAMD), Natasja Brooijmans (Wyeth), Gerard Kleywegt (University of Uppsala), Vladimir Poroikov (Russian Academy of Sciences), Christoph Helma (in silico toxicology), Ann Richard (EPA), Judy Madden (Liverpool John Moores University), Julian Tirado-Rives (Yale), Heather Carlson (University of Michigan), Joseph Tomaszewski (NCI), Joseph Contrera (FDA), Christopher Austin (NIH), Jerome Hert (UCSF), Renate Sekul (Graffinity), Gunther Stahl (Tripos), John W Liebeschuetz (CCDC), Wilfried Langenaeker (Silicos), Zsolt Zsoldos (SimBioSys), Paul Hawkins (OpenEye Scientific Software), François Delfaud (MEDIT), Anatoly Ruvinsky (University of Kansas), Robin Taylor (CCDC), Eric Jamois (Strand Life Sciences), David Gilmour (Tacit), Alex Heiphetz (Delta L Training), Frank Guerino (TraverseIT), Salvatore Alesci (Wyeth), Darius Dziuda (CCSU), Laszlo Boros (Sidmap) Fred Cohen (Fast Track Systems), Alex Tropsha (UNC), Dimitris Agrafiotis, (Johnson & Johnson), Carl Elkin (Schering-Plough)

Poster Session
We will be running poster sessions in the evenings at the meeting with themes: knowledge management (Tuesday), drug design (Wednesday) and drug development and ADMET (Thursday). This option is available to all meeting attendees. Please send your abstract and biography of ca. 300-500 words each to eCheminfo -(at)- douglasconnect.com for approval.

Program Brochure:

Download eChemProgramBrynMawr07-web2.PDF

More information at http://echeminfo.com/COMTY_conferences

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

Brochure for Autumn 2007 eCheminfo Cheminformatics Conference Available

The brochure for the eCheminfo Cheminformatics Conference is now available:

Latest Advances in Drug Discovery & Development
15-19 October 2007
Community of Practice Meeting, Autumn 2007
a joint InnovationWell and eCheminfo InterAction Meeting
Bryn Mawr College, Philadelphia
http://www.echeminfo.com/COMTY_conferences

Download the brochure as a pdf here:

Download eChemProgramBrynMawr07-web1.PDF

Look forward to seeing you there  - you will not find drug discovery informatics discussions to match these anywhere else in the world this year :)!!

Barry

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