Project Board

Experimental Project Board - please be gentle!

This is an EXPERIMENTAL page for you to add your ideas about projects. Please try it out so we can get a feel how the technology works.

Known problems

Some forms (e.g. on SG) have little TEXTAREA boxes and this makes the formatting very nasty. Also, some forms send other characters (I think VAX does) for CR. So if the output looks nasty, we'll try to code round it.

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22nd.Mar '94 - PeterMR

Appended contributions

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Please add your suggestions for projects here. This is for fairly short contributions, whilst longer ones can go to the list. If you get a group together you could post the membership here. If you get 'critical mass' we can set you up a special page just for you! Good Luck

Added by: PeterMR on Wed Mar 22 19:02:07 GMT 1995

I am planning on looking at virus capsid structure for my project. Any help or ideas will be appreciated...starting by using the basic paper by Caspar and Klug. Gail (

Added by: Gail Schuman ( on Wed Mar 22 20:10:04 GMT 1995

I'm doing a project on Bacteriorhodopsin. Preliminary stuff may be reached under "interesting links" from the PPS home page. Any takers? Iddo Friedberg

Added by: Iddo Friedberg on Thu Mar 23 07:55:17 GMT 1995

I will try to contribute something about N-linked oligosaccharides - one form of posttranslational modifications of proteins. Help, ideas, contributions from others are very much welcome ! Achim

Added by: AchimT on Thu Mar 23 12:52:05 GMT 1995

I am planning on doing my project around secondary structure prediction. Hydrophobic regions, alpha helix, beta sheets, coil prediction, etc. I will try to explain all the different prediction methods. Some methods also use multiple alignments so this will probably also be part of the project. But as I am new, but interested, in this subject it will take a while for my project to finish.

Added by: A.P.N. de Boer ( on Thu Mar 23 15:49:54 GMT 1995

I'm planning a project on NMR structure determination. I've received offers of help from Damian Moran and Peter Karuso. All other offers will be gratefully accepted.

Added by: Brendan Duggan ( on Fri Mar 24 00:38:59 GMT 1995

I'm thinking about doing a piece on SH2/SH3 protein-protein interaction domains. I have come across them in signal transduction molecules. There are good reviews on the subject, so I can get the basics together. Would anyone be interested in coming in to help me do the fancy computing as several domains have been crystallised.Also if anyone is interested in similar domains in different systems...

Added by: Nina K ( on Fri Mar 24 08:52:00 GMT 1995

Our plan this far is to present A general review of the immune system in mammals with emphasis on structures of the involved immunoglobulins. Where it will end...Is yet to be seen ;-)

Added by: Svend & Troels on Fri Mar 24 12:34:29 GMT 1995

Oups...Here is our adress: and

Added by: Svend & Troels on Fri Mar 24 12:37:40 GMT 1995

I'll gladly volunteer to help with the NMR structure determination process. I also plan to pull together a project about DNA binding domains, and would be glad to coordinate with others with the same interest.

Added by: Angie Kantola ( on Fri Mar 24 20:23:02 GMT 1995

I have volunteered to work on the "Classes of Membrane Proteins" project (cf. "families" mailing list. So far Yoni and (Janina Krauzewicz) have joined. Iddo Friedberg has offered his bacteriorhodopsin project as a resource. If anybody else has been assigned a membrane protein, please feel free to contact me at "".

Added by: Roy Lancasterroylanc on Su Mar 26 19:53:49 BST 1995

I'll do an essay on protein translocation (to cover the role of signal peptides unless someone else wants that). Any suggestions/help welcome, mail me at:

Added by: Mia Unson ( on Fri Mar 31 21:24:03 BST 1995

Hi since I have a G-protein I thought is would be nice to do hypertext pages on how to determine the E, G, and R regions of this protein from secondary structure calculations. I will probably have the pages done by the end of the first week in May

Added by: FRED-G on Mo Apr 3 00:58:34 BST 1995

I will try to contribute something about multi-phosphorylated peptides.

Added by: 4cms on Mo Apr 3 02:12:08 BST 1995

I'm interested in the question of symmetry in protein association. Any co- investigators or tips would be welcome. Does anyone have a protein that, in the crystal, forms nearly but not quite symmetrical associations?

Added by: Steve Durbin 1HC1 ( on Wed Apr 5 16:23:12 BST 1995

I am working on the structure of membrane-spanning transport proteins, one amino acid transport protein in particular. I have a sequence and have modeled several putative secondary structures. I have identified foour MSD's and am now working on the orientation of these alpha structures within the membrane. I have many resources available to me and would like someone to help. Our project involves analysis of patient DNA, modeling of putative mutant structures, assignment of domains, analysis of energy reduction models, etc. Persons who possess mutant forms of this particular protein are usually afflicted with cystinuria or suffer from cystine stones in the kidneys. I have access to a SGI workstation with LOOK, AMBER and MIDASplus at UCSF. I have worked out secondary structures at EMBL. I really need other persons to help me analyze the structures of this as-yet unnamed protein. Please email me for more info:

Added by: Jeremy Bruce ( on Fri Apr 7 03:38:03 BST 1995

I am interested in the project about DNA binding proteins.

Added by: SolomonT on Sat Apr 8 15:21:44 BST 1995

It has occurred to me th of us undergraduates could actually take our individual protein and predict all attributes of its structure including how the structure contributes to function as a senior research project for their undergraduate degree. I am in the process of checking to see if my university will alllow me to take this approach to my senior research project. Has any body else checked on the possibility of doing a seniro research project in this way?

Added by: FredG (FAGROTT@INDYVAX.IUPUI.EDU) on Mo Apr 17 18:30:38 BST 1995

I have previously volunteered to work on poly proline helices. Any help would be greatly appreciated. If there is anyone out there with proteins containing poly proline helices, i would appreciate any information you could offer //even if it is as little as the name of your protein//.

Added by: JeffreyB ( on Tue Apr 18 09:49:49 BST 1995

I would like to take a look at how sequence motifs/fingerprints relate to function and structure. My project will also incorporate a description of the resources available on the web - eg PROSITE, PRINTS, BLOCKS et al.

Added by: Emer Brizzolara on Wed Apr 19 22:13:24 BST 1995

I will try to construct a page for Serine Proteases on the Protein Family page. I would like to include modelling the active site/substrate in 3-D (Rasmol, etc).

Added by: 2alp (Bill Chestnut) on Fri Apr 28 05:14:27 BST 1995

I came across a protein "ribonuclease inhibitor" which has horse-shoe like shape, with alpha,beta structures alternating. SCOP has classified it as alpha/beta protein. Are there any structures similar in sequence or structure to that? This protein source is from porcine.

Added by: on Fri Apr 28 18:13:22 BST 1995

I will create an HTML document designed to explore signal transduction in CheY and a related bacterial protein that I study called DctD. These proteins are regulated by phosphorylation, often involving a cascade in which the phosphate moves through several proteins. CheY is one of the best studied cases to date, and DctD is dear to my own heart. An exercise will be posted for modeling DctD structure after CheY structure. The material will be posted on In addition I will post an article on using global statistical analysis of DNAse 1 footprinting to extract cooperativity and intrinsic binding energies for a two-site system (same http address).

Added by: B. Tracy Nixon on Tue May 9 23:17:25 BST 1995

I did my graduate work on the incorporation of selenomethionine in recombinant proteins and the application of the anomalous scattering of Se for MAD phasing in X-ray crystallography. For my project, I will review the "process" from growing bacteria to solving structures would be discussed along with structures that have utilized SeMet thus far. Please send me comments about what you would like to see in such a review.

Added by: John Horton on Wed May 10 19:12:29 BST 1995

This is a test. I'm really pleased how well this course has gone. Please feel freee to keep using this Peter MR (from a strange address!)

Added by: PeterMR on Mo Ju 26 15:30:00 BST 1995

I would like to apply chaos theory to analyse the differences between folded and unfolded proteins. I'm planning to use techniques developed for time series analysis so I would need experimental data, I'm thinking on time-resolved fluorescence spectroscopy or stopped-flow CD measurements (sampling time in the order of ms or less if possible). I don't have any particular preference. All data are welcomed. Paper in Nature promissed :-) if results are OK.

Added by: J.M. Zaldivar ( on Wed May 22 15:07:21 BST 1996