[Molvis-list] Additional questions

Sat Nov 20 16:35:29 EST 2004

On Fri, 19 Nov 2004, Trans-Laboratory -- Chemical Analysis Service Provider -- wrote:

>Dear Dan, 
>
>Did those slides mentioned below get posted somewhere?  Thank you in
>advance
>
>Ricardo A. Correa C.
>Molecular Biology amateur

Thanks for the reminder Ricardo! I finally submitted the slides in PDF
format (with the original .PPT as the 'source code') to
BioMoleculesAlive.org. I haven't heard anything back from the guys there,
so I assume the slides are still under review. Their were a few delays
caused by teething problems at that site, but hopefully they have all been
worked out and (unless I have to re-write :) the slides will appear
here...

http://www.biomoleculesalive.org/browse/step2_ViewDiscipline.php?strType=Visual&strTypeName=Visual+Resources&strTypeURL=http%3A%2F%2Fwww.biomoleculesalive.org%2Fbrowse%2Fstep1_visual.php&strDiscipline=fundamental

under the "Fundamental Concepts" category. 

I am sure it would be easy for someone to do a better job of the slides I
made (explaining how structural homology can be used to link distantly
related sub-families under the 'superfamily' umbrella), but I did get
quite a good response from the audience.

Submitting to www.BioMoleculesAlive.org was quite painless, and I would do
it again. Given the amount of feedback I got from my original request it
would seem like we could easily flesh out the framework they have put in
place if people start submitting.

All the best,
Dan.

>
>Cheers!
>
>Dan.
>
>On Sat, 9 Oct 2004, Gabe McCool wrote:
>
>>Dan-
>>
>>Sounds great...looking forward to seeing your slides at some point.  
>>Further to Eric Martz's FtsZ suggestion, the presentation at
>>
>>http://www.umass.edu/microbio/chime/pipe/ftsz/present/index.htm
>>
>>tries to point out FtsZ's close structural alignment with tubulin 
>>contrasted with the low seq identity (<20%) between aligned FtsZ + tubulin
>aa
>>sequences.   Hope its helpful in some regard.
>>
>>
>>Gabe McCool
>>
>>
>>
>>
>>> From: Eric Martz <emartz at microbio.umass.edu>
>>> Reply-To: <rasmol at lists.umass.edu>
>>> Date: Fri, 08 Oct 2004 17:40:02 -0400
>>> To: <rasmol at lists.umass.edu>
>>> Subject: Re: Slides to demonstrate conservation of protein structure?
>>> 
>>> At 10/8/04, Dan Bolser <dmb at mrc-dunn.cam.ac.uk> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I would like to demonstrate the well known principal that protein 
>>>> structure is more conserved than protein sequence in evolutionary 
>>>> time. I am presenting to a group of structural biologists, so I want 
>>>> to emphasize the bioinformatic perspective.
>>>> 
>>>> My idea for a series of slides is this
>>>> 
>>>> 1) show two clearly structurally similar (same topology) protein
>domains.
>>> 
>>> One example pointed out to me years ago by Gabe McCool is the 
>>> bacterial cell division protein FtsZ. A structure-based search turns 
>>> up tubulin, but the sequence identity is only 16% (if I recall).
>>> 
>>> This paper by Friedberg, Kaplan and Margalit 
>>> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&
>>> dopt=Abst
>>> ract&list_uids=11152139
>>> assesses
>>> "the accuracy of PSI-BLAST alignments on a stringent database of 123 
>>> structurally similar, sequence-dissimilar pairs of proteins, by 
>>> comparing them to the alignments defined on a structural basis."
>>> 
>>> I will be quite interested in your slides when they become available!
>>> Please keep us posted.
>>> -Eric Martz
>>> 
>>>> 1.1) show that the two sequences are very different, and result in
>>>>      a 'bad' sequence alignment (somehow visually).
>>>> 
>>>> 2) Show a nieve (and hopefully bad) structural alignment of the two
>>>>    domains based (nievely) on the sequence alignment.
>>>> 
>>>> 3) Show a pure (and simple) structural alignment of the two domains.
>>>> 3.1) Show the sequence alignment based on the good structural alignment.
>>>> 
>>>> 
>>>> My idea is to convey the importance of structure in recognizing 
>>>> distant homology between domains.
>>>> 
>>>> I want to use a real example using real tools, but I am not sure how 
>>>> / which tools to use.Any suggetions? Good demo / bad demo? Naturally 
>>>> I need this done by yesterday, so the simpler the tools the better.
>>>> 
>>>> I will be happy to post the slides somewhere appropriate to share 
>>>> this work with the world.
>>>> 
>>>> All the best,
>>>> Dan. 
>
>-----Original Message-----
>From: molvis-list-admin at bioinformatics.org
>[mailto:molvis-list-admin at bioinformatics.org] On Behalf Of Dan Bolser
>Sent: 19 November 2004 16:41
>To: molvis-list at bioinformatics.org
>Subject: Re: [Molvis-list] Additional questions
>
>
>My favourite bond prediction server is ...
>
>http://www.mrc-lmb.cam.ac.uk/genomes/nci/
>
>However, it looks down for the time being.
>
>
>Here is the reference...
>
>http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=168935
>
>It predicts canonical bonds as well as 'non-canonical', but not
>electrostatic interactions (as far as I know).
>
>
>Predicting quaternary structure is a big field, with many different groups
>trying many different approaches. I would suggest you ask your question here
>
>pdb-l at rcsb.org
>
>All the best,
>Dan.
>
>
>On Thu, 18 Nov 2004, [iso-2022-jp] $BHSDM(B $B at 2@8(B wrote:
>
>>Dear members
>>
>>Some times ago, I asked you about H-bonds visualization in homodimer.
>>But I had additional questions following below.
>>
>>1.How to detect monomer-monomer interactions, H-bonds, hydrophobic
>>   interactions and electrostatic interactions etc. And Which
>>visualization-
>>   tool is best for visualizing them?
>>
>>2.Are there any tools to predict quaternary structures and it's interaction
>>   sites from tertiary structures?
>>
>>Tell me please.
>>
>>>From H.Iiduka
>>
>>e-mail: haruo_ii at hotmail.com
>>
>>_________________________________________________________________
>>$B3Z$7$$3(J8;z$G%3%3%mEA$o$k%a%C%;%s%8%c!<(B 
>>http://messenger.msn.co.jp/
>>
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>
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