[Molvis-list] Additional questions

Fri Nov 19 17:39:00 EST 2004

Dear Dan, 

Did those slides mentioned below get posted somewhere?  Thank you in advance

Ricardo A. Correa C.
Molecular Biology amateur

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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