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

Program/Schedule for European eCheminfo InterAction meeting (9,10 November 2005)

The European eCheminfo InterAction meeting "Applications of Cheminformatics and Chemical Modelling to Drug Discovery" takes place in Basel, Switzerland next week (November 9-10).  The schedule with list of presentations and discussion sessions is available at:
http://echeminfo.colayer.net/files/SpeakerTopcSchedule-IA05-Basel-v5.pdf

The eCheminfo meeting runs concurrently with our InnovationWell Community meeting; registrants are welcome to attend sessions from either program.  Further details, such as abstracts and speaker bios, can be viewed in the Program areas of either the http://innovationwell.net/ or the echeminfo.com websites.

We will be closing registrations shortly, so please let us know quickly if you'd like to come.  Register through the websites or contact Nicki Douglas (nicki.douglas at douglasconnect.com, +41 61 851 04 61)

And if you can't make the meeting, you can access the recordings and presentation materials if you become a member of one of these communities. You will also have access to all previous sessions (including those from last month's US InterAction meetings in Philadelphia being released this month).

Best regards,
Barry Hardy
Community of Practice Manager
Douglas Connect, Switzerland
tel: +41 61 851 0170

InnovationWell eCheminfo meeting workshop conference management executive drug safety KM Life Sciences Pharma Drug Discovery Drug Development Healthcare Innovation Informatics cheminformatics Knowledge Management Molecular Modelling events

eCheminfo and InnovationWell Autumn 2005 Program

I summarise below the list of sessions with over 100 top speakers and discussion leaders for the program listing for the upcoming Autumn InterAction Meetings taking place in Philadelphia and Basel. Please add a traceback or link for other like-minded folk to find!

I also provide an electronic brochure for download here for the InnovationWell Autumn Program on Knowledge-based Innovation in Life Science Product Development:
http://barryhardy.blogs.com/theferryman/files/InnovationWell-ProgramAutumn05.PDF

And the equivalent eCheminfo brochure on Drug Discovery:
http://barryhardy.blogs.com/theferryman/files/eCheminfo-ProgramAutumn05.pdf

Note: The poster sessions will be run as electronic poster sessions using tabletop spaces, a wireless network and Internet facilities at the meetings, in addition to virtual access through the website, i.e., the posters will be electronic but the access can be face-to-face or virtual. You can participate in person and virtually in the poster sessions.  We can supply nourishment and refreshments locally; remote participants may have to order out! [We also expect, subject to on-site testing, to have live conference call capabilities for remote participating members to join local discussions.]  Anyone interested in presenting such an "electronic poster" should directly contact us via email at innovationwell at douglasconnect.com

Look forward to seeing you in Philadelphia or Basel!

Barry Hardy
Community of Practice Manager
Douglas Connect
http://douglasconnect.com/
+41 61 851 0170 (office)

InnovationWell & eCheminfo InterAction Meetings
Philadelphia, US, 11-12 October 2005 and Basel, Switzerland, 9-10 November
List of Sessions with Speakers & Schedule (InterAction Autumn Meetings)
http://innovationwell.net/ and http://echeminfo.com/

Registration to attend the meetings or to access virtually is available through the websites or through contacting Nicki Douglas [nicki.douglas at douglasconnect.com]

InnovationWell eCheminfo meeting workshop conference management executive drug safety KM Life Sciences Pharma Drug Discovery Drug Development Healthcare Innovation Informatics cheminformatics Knowledge Management events

…PROGRAM LISTING CONTINUING IN FULL POSTING…..

eCheminfo Autumn 2005 Program Brochure - Cheminformatics & Modeling Applications in Drug Discovery

Here is a copy of the Program Brochure for our eCheminfo Autumn 2005 Program on Cheminformatics & Modeling Applications in Drug Discovery including our US InterAction Meeting in Philadelphia 11,12 October 2005 and our European meeting in Basel 9,10 November 2005:

Download eCheminfo-ProgramAutumn05.pdf

Barry Hardy
eCheminfo Community of Practice Manager
Douglas Connect, Switzerland
+41 61 851 0170 (office)

eCheminfo LinkedIn Networking Group

One of our primary goals with the eCheminfo Community of Practice is to provide an opportunity for focused professional peer-to-peer networking for those with interests in drug discovery informatics,  modelling and design.  It is hard to beat face-to-face meetings for networking and for that we hope you can make our InterAction Meetings in Philadelphia 11-12 October ’05 and in Basel 9-10 November ’05 (Program information on the meetings is being updated in the Program area of http://eCheminfo.com/)

We have also been piloting use of the LinkedIn service as a new networking tool for the group.  This is a useful tool for discovering more about other peer professionals with like interests and making contacts.

To join the eCheminfo community and to take advantage of this networking service simply complete the following two steps:

1) Complete the eCheminfo SignUp available at http://eCheminfo.com/.

2) Use the link below to join, and hence be able to make direct contact (within our and LinkedIn's carefully considered privacy guidelines and controls) with group members on queries, ideas, opportunities and proposals together.

Whether you use LinkedIn already or are new to LinkedIn, please join the members-only eCheminfo Group here (It is only one step away) by clicking on the following link:

https://www.linkedin.com/e/gis/1173/77EB680070FF/
(or by pasting it into your Web browser)

Please note that all members are either pre- or post-approved by me.

Through the members-only eCheminfo Group you can:

- Leverage the power of the eCheminfo network to find and reach the new contacts you need
- Accelerate your career through referrals from eCheminfo members
- Know more than a name: view rich professional profiles from fellow eCheminfo members
- Let other eCheminfo members know what you have to offer to them and their contacts
- Limit your network searches to other eCheminfo members only, if and when you wish to do so

Access to special eCheminfo features on LinkedIn is currently free of cost or financial obligations, and is available to eCheminfo members only. Any changes to this policy affecting an individual's service will be first subject to my and the individual member's explicit approval.

Barry Hardy
eCheminfo Community of Practice Manager
Douglas Connect, Switzerland
+41 61 851 0170 (office)

eCheminfo pharma LinkedIn Drug Discovery cheminformatics science conference events

CFP: Posters, Contributed talks, Bursaries for eCheminfo Autumn meetings on Drug Discovery

Poster Abstracts for eCheminfo Autumn InterAction Meetings should be submitted as soon as possible and at the latest by: 15 August ’05 for US meeting posters; 31 August ’05 for European meeting posters.

Posters can be on any informatics or modeling topic (and can also be combined with experimental approaches) of relevance to Drug Discovery.

Poster Abstracts (ca. 300 words) should be sent to eCheminfo at douglasconnect.com

We will select a number of contributed talks to be presented at the meetings based on abstracts submitted.  We also have sponsorship requests under review to support travel bursaries for a selection of young academic investigators to attend the meeting based on submitted abstract.

Papers submitted related to poster presentations or talks will be refereed for consideration for publication in a special Drug Discovery issue of the Molecular Simulation journal.  Deadline for paper submission: 31 October ’05 for US meeting; 30 November ’05 for European meeting posters.

Subscribed members who cannot attend the meetings in Philadelphia or Basel in person will be able to access all meeting presentations with audio and to submit posters through the eCheminfo website. 

You must also have completed your annual membership subscription or meeting registration in time through the Online Ticket Office available after login to http://echeminfo.com/ so that access rights or a meeting place reservation are provided for you.   Alternatively contact Nicki Douglas (nicki.douglas at douglasconnect.com, +41 61 851 0461) for support.  Academic and group rates are available.

Barry Hardy
eCheminfo Community of Practice Manager
Douglas Connect, Switzerland
+41 61 851 0170 (office)

eCheminfo US Autumn 2005 InterAction Meeting:  Applications of Cheminformatics & Chemical Modelling to Drug Discovery
October 11-12, Bryn Mawr College, Philadelphia, USA
and
eCheminfo European Autumn 2005 InterAction Meeting:  Applications of Cheminformatics & Chemical Modelling to Drug Discovery
November 9-10, Swissotel L’entrée Conference Center, Basel, Switzerland

You can view meeting abstracts in the Program area of http://echeminfo.com/

eCheminfo pharma Drug Discovery cheminformatics Molecular Simulation conference meeting science chemistry events

eCheminfo European Autumn 2005 InterAction Meeting

The eCheminfo European Autumn 2005 InterAction Meeting will be taking place at the Swissotel L’entrée Conference Center, Basel, Switzerland, Nov 9-10.  Program information and registration is available through the eCheminfo website at http://echeminfo.com/

The theme of the meeting is the application of cheminformatics and chemical modelling to drug discovery and will include the following sessions:

Virtual Screening, Docking & Scoring, chaired by Miklos Vargyas (ChemAxon); Web-based Services in Drug Design, chaired by Kim Henrick (European Bioinformatics Institute); Computational Biochemistry, chaired by Alessandro Curioni (IBM Zurich); Applications of Machine Learning & Graph Mining in Drug Discovery, chaired by Stefan Kramer (Technische Universitaet Muenchen); Biosensors & Nanofluidics, Nick Quirke (Imperial College London); Protein Folding and Dynamics, chaired by Wilfred van Gunsteren (ETH-Zurich)

Invited Speakers include:
Graham Richards (University of Oxford), Xavier Barril (Vernalis), Amedeo Caflisch (ETH-Zurich), David Morley (Enspiral Discovery Ltd), Didier Rognan (University of Strasbourg), Dimitris Dimitropoulos (European Bioinformatics Institute), Johann Gasteiger (Universitaet Erlangen-Nuernberg), Simon Coles (University of Southampton), Eugene Krissinel (European Bioinformatics Institute), Torsten Schwede (University of Basel), Paul Tavan (University of Munich), Ursula Roethlisberger (Swiss Federal Institute of Technology, Lausanne), Alessandro Curioni (IBM Zurich), Ian Williams (University of Bath), Gerald Monard (Universite Henri Poincare – Nancy), Ken Merz (QuantumBio), Nick Quirke (Imperial College London), Richard Gilbert (E2v Technologies), Andrew De Mello (Imperial College London), Jens Walther (ETH-Zurich), Christoph Helma (University of Freiburg), Peter Willett (University of Sheffield), Joost N. Kok (Leiden University), Gisbert Schneider (Johann Wolfgang Goethe-University), Michael Berthold (University of Konstanz), Jeremy Smith (University of Heidelberg), Wolfgang Wenzel (University of Karslruhe), Thomas Kiefhaber (University of Basel), Xavier Daura (University of Barcelona), Nikolay V. Dokholyan (University of North Carolina), Michele Vendruscolo (University of Cambridge)

The eCheminfo meetings will have exhibitor tables for software demos and evening poster sessions; posters will also be available for viewing through the website.  Posters can be on any informatics or modeling topic of relevance to drug discovery. Those who cannot make the meetings are also able to register to access all presentations, posters and discussions through the eCheminfo website. Registrants for the European meeting will also be able to access the full proceedings with audio of the equivalent US meeting being held in Philadelphia.

Poster Abstracts (ca. 300 words) should be sent to eCheminfo at douglasconnect.com

The InnovationWell European community of practice Autumn meeting will be taking place at the same location and on the same dates as the eCheminfo European meeting.  This meeting will be covering semantic web applications in drug discovery and development, life science intellectual property management and valuation; knowledge management and transfer in R&D and manufacturing, clinical trial productivity, drug safety knowledge management and predictive toxicology.  All eCheminfo registrants will also have access to the InnovationWell meeting activities. (See http://innovationwell.net/ for more details).

Please register early for the meetings as the number of places are limited.  You can register for the meeting on the website or contact Nicki Douglas (nicki.douglas at douglasconnect.com, +41 61 851 0461) to reserve your place.

Barry Hardy
Community of Practice Manager
Douglas Connect

eCheminfo US Autumn 2005 InterAction Meeting

The eCheminfo US Autumn 2005 InterAction Meeting will be taking place at Bryn Mawr College, Philadelphia, US, 11-12 October.  Program information and registration is available through the eCheminfo website at http://echeminfo.com/

The theme of the meeting is the application of cheminformatics and chemical modelling to drug discovery and will include the following sessions:

Virtual Screening, Docking & Scoring, chaired by Max Cummings (Johnson & Johnson); Web-based Services in Drug Design, chaired by Marc Nicklaus, (National Institutes of Health); Protein Folding, Misfolding & Aggregation: Applications to Disease, chaired by Nikolay V. Dokholyan (University of North Carolina); New Developments in Biophysical Applications of Quantum Mechanics, chaired by Ken Merz/Lance Westerhoff (QuantumBio); Simulation of Membranes & Ion Channels, co-chaired by Richard Pastor (FDA) & Michael Klein (University of Pennsylvania)

Invited Speakers include:
Emanuele Perola (Vertex), Mark McGann (Openeye), John Irwin (UCSF), Renee DesJarlais (Johnson & Johnson), Willem Nissink (Cambridge Crystallographic Data Centre), Brad Feuston (Merck), Brett Tounge (Johnson & Johnson), Steve Bryant (NCBI), David Covell (NCI), Andrew Miranker (Yale University), David Teplow (David Geffen School of Medicine at UCLA), Ron Wetzel (University of Tenessee Medical Center), Michael Thorpe (Arizona State University), Feng Ding (University of North Carolina), Mike Pitman (IBM), Jeff Klauda (NIH), Emad Tajkhorshid (Beckman Institute, University of Illinois at Urbana-Champaign), Richard Pastor (FDA), Preston Moore (USIP), Jian Li (Johnson & Johnson), Martin Peters (Penn State), Darrin York (University of Minnesota)

The eCheminfo meetings will have exhibitor tables for software demos and evening poster sessions; posters will also be available for viewing through the website.  Posters can be on any informatics or modeling topic of relevance to drug discovery. Those who cannot make the meetings are also able to register to access all presentations, posters and discussions through the eCheminfo website. Registrants for the US meeting will also be able to access the full proceedings with audio of the equivalent European meeting being held in Basel, Switzerland.

Poster Abstracts (ca. 300 words) should be sent to eCheminfo at douglasconnect.com

The InnovationWell US community of practice Autumn meeting will be taking place at the same location and on the same dates as the eCheminfo US meeting.  This meeting will be covering semantic web applications in drug discovery, personalised medicine, knowledge management and transfer in R&D, clinical trial productivity, drug safety knowledge management and predictive toxicology.  All eCheminfo registrants will also have access to the InnovationWell meeting activities. (See http://innovationwell.net/ for more details).

Please register early for the meetings as the number of places are limited.  You can register for the meeting on the website or contact Nicki Douglas (nicki.douglas at douglasconnect.com, +41 61 851 0461) to reserve your place.

Barry Hardy
Community of Practice Manager
Douglas Connect

eCheminfo Autumn 2005 InterAction Meetings

The focus of the eCheminfo Autumn 2005 InterAction Meetings on Applications of Cheminformatics & Chemical Modelling to Drug Discovery is to bring together world-class researchers working in the drug discovery field, and have them present recent cutting-edge research results. The meetings are intended to bring together researchers in both industry, government and academia and on an international basis.  Both US and European meetings will be held in key pharma and life science centers of activity in the US and Europe.  The emphasis of these community of practice meetings and format is on communication, discussion and networking, leading to new opportunities, collaborations and best practices. 

All sessions will involve presentations from leading invited researchers, roundtable discussions, and poster sessions and software demonstrations running on a local wireless network.  All presentations from both meetings will be available to registrants for remote access through the eCheminfo website. SignUp and registration for the meetings can be completed through the eCheminfo website.

Philadelphia, US, Oct 11-12

Virtual Screening, Docking & Scoring, chaired by Max Cummings (Johnson & Johnson)

Web-based Services in Drug Discovery, chaired by Marc Nicklaus (National Institutes of Health)

Protein Folding, Misfolding & Aggregation: Applications to Disease, chaired by Nikolay V. Dokholyan (University of North Carolina)

New Developments in Biophysical Applications of Quantum Mechanics, chaired by Ken Merz and Lance Westerhoff (QuantumBio)

Simulation of Membranes & Ion Channels, co-chaired by Richard Pastor (FDA) and Michael Klein (University of Pennsylvania)

Basel, Switzerland, Nov 9-10

Web-based Services in Drug Discovery, chaired by Kim Henrick (European Bioinformatics Institute)

Computational Biochemistry, chaired by Alessandro Curioni (IBM Zurich)

Fluid Flow in Nanopores, chaired by Nick Quirke (Imperial College London)

Applications of Machine Learning & Graph Mining in Drug Discovery, chaired by Stefan Kramer (Technische Universitaet Muenchen)

Protein Folding and Dynamics, chaired by Wilfred van Gunsteren (ETH-Zurich)

Barry Hardy
eCheminfo Community of Practice Manager
eCheminfo.com

Structure, Function, Self-assembly and Origin of Simple Membrane Proteins

Andrew Pohorille, head of the NASA Center for Computational Astrobiology and Fundamental Biology, will present the following seminar at the eCheminfo 2004 Web conference (http://echeminfo.com), starting 8 November 2004.

Structure, Function, Self-assembly and Origin of Simple Membrane Proteins

Integral membrane proteins perform such essential cellular functions as transport of ions, nutrients and waste products across cell walls, transduction of environmental signals, regulation of cell fusion, recognition of other cells, energy capture and its conversion into high-energy compounds. In fact, 30% of genes in modern organisms codes for membrane proteins.

Although contemporary membrane proteins or their functional assemblies are quite complex, their transmembrane fragments are remarkably simple. Their most common structural motif is a bundle of alpha-helices. In a series of molecular dynamics computer simulations we investigated self-organizing properties of simple membrane proteins based on this structural motif. Specifically, we studied folding and insertion into membranes of short, nonpolar or amphiphatic peptides. We also investigated glycophorin A, a peptide that forms sequence-specific dimers, and a transmembrane aggregate of four identical alpha-helices that forms an efficient and selective voltage-gated proton channel.

Many peptides are attracted to water-membrane interfaces. Once at the interface, nonpolar peptides spontaneously fold to alpha-helices. Whenever the sequence permits, peptides that contain both polar and nonpolar amino also adopt helical structures, in which polar and nonpolar amino acids are immersed in water and membrane, respectively. Specific identity of side chains is less important. Helical peptides at the interface could insert into the membrane and adopt a transmembrane orientation. This is, however, unfavorable because polar groups in the peptide become completely dehydrated.
The unfavorable free energy of insertion can be regained through association of helices in the membrane. These helical bundles could form channels capable of transporting ions and small molecules across membranes. Stability of transmembrane aggregates of simple proteins is often only marginal and, therefore, it can be regulated by environmental signals or small sequence modifications.

A key step in the earliest evolution of membrane proteins was the emergence of selectivity for specific substrates. Many channels could become selective if one or only a few properly chosen amino acids are properly placed along the channel, acting as filters or gates. This is a convenient evolutionary solution because it does not require imposing conditions on the whole sequence.

Barry Hardy
Douglas Connect
www.douglasconnect.com
Cheminformatics & Chemical Modelling in Drug Discovery: echeminfo.com
Cheminfostream Blog: http://barryhardy.blogs.com/cheminfostream/