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/ > >_______________________________________________ >Molvis-list mailing list >Molvis-list at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/molvis-list > _______________________________________________ Molvis-list mailing list Molvis-list at bioinformatics.org https://bioinformatics.org/mailman/listinfo/molvis-list