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An ACS in (not so) Sunny San Diego

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Another ACS National meeting is over, this time in San Diego. It was good to catch up with old friends and meet many new, interesting people. As I was there for a relatively short period, I bounced around most sessions.

MEDI and COMP had a joint session on desktop modeling and its utility in medicinal chemistry. Anthony Nicholls gave an excellent talk, where he differentiated between “strong signals” and “weak signals”, the former being extremely obvious trends, features or facts that do not require a high degree of specialized exerptise to detect and the latter being those that do require significantly more expertise to identify. An example of a strong signal would be an empty region of a binding pocket that is not occupied by a ligand feature – it’s pretty easy to spot this and when hihglighted the possible actions are also obvious. A weak signal could be a pi-stacking interaction which could be difficult to identify in a crowded 3D diagram. He then highlighted how simple modifications to traditional 2D depictions can be used to make the obvious more obvious and make features that might be subtle, say in 3D, more obvious in a 2D depiction. Overall, an elegant talk, that focused on how simple visual cues in 2D & pseudo-3D depictions can key the mind to focus on important elements.

There were two other symposia that were of particular interest. On Sunday Shuxing Zhang and Sean Eakins organized a symposium on polypharmacology with an excellent line up of speakers including Chris Lipinski. Curt Breneman gave a nice talk that highlighted best practices in QSAR modeling and Marti Head gave a great talk on the role and value of docking in computational modeling projects.

On Tuesday, Jan Kuras and Tudor Oprea organized a session on System Chemical Biology. Though the session appeared to be more on the lines of drug repurposing, there were several interesting talks. Ebelebola May from Sandia Labs gave a very interesting talk on a system level model of small molecule inhibition of M. Tuberculosis and F. Tularensis - combining metabolic pathway models and cheminformatics.

John Overington gave a very interesting talk on identifying drug combinations to improve safety. Contrary to much of my reading in this area, he points out the value of “me-too” drugs and taking combinations of such drugs. Given that such drugs hit the same target, he pointed out that this results in the fact that off-targets will see reduced concentrations of the individual drugs (hopefully reducing side effects) while the on-target will see the pooled concentration (thus maintaining efficacy (?)). It’s definitely a contrasting view to the one where we identify combinations of drugs hitting different targets (which I’d guess is a tougher proposition, since identifying a truly synergistic combination requires a detailed knowledge of the underlying pathways and interactions). He also pointed out that his analyses indicated that combination dosing is not actually reduced, in contrast to the current dogma.

As before we had a CINFlash session which I think went quite well – 8 diverse speakers with a pretty good audience. The slides of the talks have been made available and we plan to have another session in Philadelphia this Fall, so consider submitting something. We also had a great Scholarships for Scientific Excellence poster session – 15 posters covering topics ranging from reaction prediction to an analysis of retractions. Excellent work, and very encouraging to see newcomers to CINF interested in getting more invovled.

The only downsides to the meeting was the chilly and unsunny weather and the fact that people still think that displaying tables of numbers in a slide actually transmits any information!

Written by Rajarshi Guha

April 6th, 2012 at 2:39 am

Posted in Uncategorized

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A New Round of Lightning Talks

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With the 2011 Fall ACS meeting coming up in Denver next month, CINF will be hosting another round of lightning talks – 8 minutes to talk about anything related to cheminformatics and chemical information. As before, these talks won’t be managed via PACS, as a result of which we are taking short abstracts between July 14 and Aug 14.We hope that we’ll get to hear about interesting and recent stuff. Remember, this is meant to be a fun event so be creative! (You can see slides from the first run of this session last year).

The full announcement is below:

For the 2011 Fall meeting in Denver (Aug 28 – Sep 1), CINF will be running an experimental session of lightning talks – short, strictly timed talks. The session does not have a specific topic, however, all talks should be related to cheminformatics and chemical information. One of the key features of this session is that we will not be using the traditional ACS abstract submission system, since that system precludes the inclusion of recent work in the program.

So, since we will be accepting abstracts directly, the expectation is that they be about recent work and developments, rather than rehashes of year-old work. In addition, talks should not be verbal versions of posters submitted for this meeting. Given the short time limits we don’t expect great detail – but we are expecting compact and informative presentations.

That’s the challenge.

What

  • Talks should be no longer than 8 minutes in length. At 8 minutes, you will be asked to stop.
  • Use as many slides as you want, as long as you can finish in 8 minutes
  • Talks should not be rehashes of poster presentations
  • Talks will run back to back, and questions & discussion will be held of off until the end

If you haven’t participated in these types of talks before here are some suggestions:

  • No more than three slides for a 5 minute talk (but if you can pull of 20 slides in 8 minutes, more power to you)
  • Avoid slides with too much text (and don’t paste PDF’s of papers!)
  • A single chart per slide and make sure labels are readable at a distance

When

1:30pm, Wednesday, August 31st, 2011

Submissions run from July 14 to Aug 14

Where

Room 112, Colorado Convention Center

How

  • Send in an abstract of about 100 – 120 words to cinf.flash@gmail.com
  • We will let you know if you will be speaking by Aug 21 and we will need slide decks by Aug 24
  • You must be registered for the meeting
  • Note that the usual publication/copyright rules apply
  • We will encourage live blogging and tweets (if we have net access)

Written by Rajarshi Guha

July 22nd, 2011 at 4:28 am

Posted in cheminformatics

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Call for Papers: High Content Screening: Exploring Relationships Between Small Molecules and Phenotypic Results

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242nd ACS National Meeting
Denver, Aug 28 – Sept 1, 2011
CINF Division

Dear Colleagues, we are organizing an ACS symposium, focusing on the use of High Content Screening (HCS) for small molecule applications. High content screens, while resource intensive, are capable of providing a detailed view of the phenotypic effects of small molecules. Traditional reporter based screens are characterized by a one-dimensional signal. In contrast, high content screens generate rich, multi-dimensional datasets that allow for wide-ranging and in-depth analysis of various aspects of chemical biology including mechanisms of action, target identification and so on. Recent developments in high-throughput HCS pose significant challenges throughout the screening pipeline ranging from assay design and miniaturization to data management and analysis. Underlying all of this is the desire to connect chemical structure to phenotypic effects.

We invite you to submit contributions highlighting novel work and new developments in High Content Screening (HCS), High Content Analysis (HCA), and data exploration as it relates to the field of small molecules. Topics of interest include but are not limited to

  • Compound & in silico screening for drug discovery
  • Compound profiling by high content analysis
  • Chemistry & probes in imaging
  • Lead discovery strategies – one size fits all or horses for courses?
  • Application of HCA in discovering toxicology screening strategies
  • Novel data mining approaches for HCS data that link phenotypes to chemical structures
  • Software & informatics for HCS data management and integration
In addition to these topics special consideration will be given to contributions that present contributions in in-silico exploration based on HCS data. We would also like to point out that sponsorship opportunities are available. The deadline for abstract submissions is April 1, 2011. All abstracts should be submitted via PACS at http://abstracts.acs.org. If you have any questions feel free to contact Tim or myself.

Tim Moran
Accelrys
tmoran@accelrys.com
+1 858 799 5609

Rajarshi Guha
NIH Chemical Genomics Center
guhar@mail.nih.gov
+1 814 404 5449

Written by Rajarshi Guha

March 24th, 2011 at 12:26 pm

Posted in research,software

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Back from Boston

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Another ACS National Meeting, this time in Boston, is over and I’m finally home. I gave two talks, one on issues surrounding the data deluge in modern drug discovery and another one on structure activity landscapes. There were a number of great sessions in CINF, COMP and MEDI, with some thought-provoking talks. I especially liked a talk given by Birte Seebeck, in which they abstracted the idea of SALI (which focuses on structural features of ligands) to one that considers interactions betwen a ligand and a receptor – thus identifying activity hotspots within a protein site that actually cause the activity cliffs. The idea is somewhat similar to SiFT’s, but differs in that it takes into account the SAR. (As a side note, I discovered that one of our landscape papers is in the Top 25 in Drug Discov. Today). Gerry Maggiora gave a very thought provoking talk on the topic of activity cliffs,  highlighting the fact that there’s a lot of open questions that need to be looked at in this area. Ant Nicholls of spoke on the disconnect between molecular modeling in academia industry. His three suggestions: rigorous statistics training, stop government funding for all but basic research and all remaining funding must have an experimental component.

I also met up with a number of old friends, met some people with whom I’d only had email or FriendFeed conversations and made new friends. We had a Blue Obelisk dinner, with Christoph awarding a Blue Obelisk to Nina Jeliazkova. This time round, we got a whole restaraunt to ourselves, thanks to Christoph, so conversations was much easier! Also the financial contribution towards the dinner from Bob Belford and Harry Pence was very much appreciated.

At this meeting I finally got round to making use of Twitter – it turns out it was quite useful for keeping running notes during a talk, as well as keeping track of other parallel sessions. Thanks to Egon for those extra tweets (though maybe Egon and I were being a bit obssesive!?). A quick hack I put together just before the meeting allowed Tweeters to visualize the Twitter stream emanating from the ACS meeting as a word cloud. Obviously, it works better with more people tweeting, but cute nonetheless.

As always, CINF hosts some great receptions and this meetings’ ones were no exception. Though the weather didn’t cooperate, the convention center was pretty nice in providing free wireless. This came in especially useful as we had a speaker with three talks in our program but was unable to make it to the meeting. With the wireless available, we successfully connected with him over Skype, and with me switching slides, were able to have him present (audio and video) his work. Definitely not a trend we want to encourage, but for emergencies, “Skype talks” are great!

At this meeting I also organized an experimental symposium consisting of lightning talks – 8 minutes talks on arbitrary (but hopefully interesting) topics in chemical information and cheminformatics. While we only had 5 speakers, we had a great set of talks – I’m still amazed at how Richard West got through 24 slides in 7 minutes so smoothly! While it could have been publicized better, we got a lot of good feedback and will be running a revamped version in Denver, next fall.

Overall a pretty good meeting, and my last meeting as CINF Program Chair. I had a great time in this role, and with the help of a very capable Program Committee, I think we were able to successfully develop interesting multidisciplinary programs over the last four meetings. As I step down, Rachelle Bienstock from the NIEHS will take over as Program Chair, and I wish her all the best. However, I’m not done with CINF just yet :) I’ve been elected as Chair-Elect of CINF for 2011 so will be switching roles (though I certainly hope to continue contributing to the CINF program in the future).

I’ll end with three suggestions for the ACS: 1. Seriously consider letting divisions to drop Thursdays 2. Reduce registration fees & do a better job on hotel rates 3. Fix the meetings to one or two places (preferably San Francisco).

Update: I had misstated Anthony Nicholl points from his presentation. The post is updated to the correct that.

Written by Rajarshi Guha

August 27th, 2010 at 2:54 am

Posted in cheminformatics

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CINFlash Deadline Approaching

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One more week to go (Aug 7 is the deadline) to put in short abstracts for the CINFlash lightning talk symposium at the fall ACS meeting in Boston this month. This is your chance for 6 minutes of fame!

Written by Rajarshi Guha

August 2nd, 2010 at 2:17 pm

Posted in Uncategorized

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