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Useful links

Before we start, here a few hyperlinks that you may want to check out (or bookmark) before, during or after this practical. Some of these links will be available on every page of the practical in the pink box above.

Abstract of the JMB paper

As the structural database continues to expand, new methods are required to analyse and compare protein structures. Whereas the recognition, comparison, and classification of folds is now more or less a solved problem, tools for the study of constellations of small numbers of residues are few and far between. In this paper, two programs are described for the analysis of spatial motifs in protein structures. The first, SPASM, can be used to find the occurrence of a motif consisting of arbitrary main-chain and/or side-chains in a database of protein structures. The program also has a unique capability to carry out "fuzzy pattern matching" with relaxed requirements on the types of some or all of the matching residues. The second program, RIGOR, scans a single protein structure for the occurrence of any of a set of pre-defined motifs from a database. In one application, spatial motif recognition combined with profile analysis enabled the assignment of the structural and functional class of an uncharacterised hypothetical protein in the sequence database. In another application, the occurrence of short left-handed helical segments in protein structures was investigated, and such segments were found to be fairly common. Potential applications of the techniques presented here lie in the analysis of (newly determined) structures, in comparative structural analysis, in the design and engineering of novel functional sites, and in the prediction of structure and function of uncharacterised proteins.

So ... what is it ?

SPASM is a program (or, rather, a set of programs) with which you can find out if a (usually small) set of residues that you find interesting (for whatever reason) occurs in a similar spatial constellation in any other known protein structures. The software is completely general, in that you, the user, can define your own set of "interesting" residues by simply putting them in a small PDB file and using that as input to the software (together with values for a number of program parameters; but don't worry about those yet).

What kinds of spatial arrangements ("3D motifs") could you possibly find "interesting" ? Well, for instance:

The major limitation at present is that only protein residues can be included in a 3D motif; nucleic acids and hetero-entities cannot be handled.

Besides this form of motif recognition, one can also envisage working the other way around. In other words, one could construct a large database of motifs that have some well-defined functional and/or structural relevance, and then scan each newly determined protein structure against that database. The results may well provide clues as to the function of the new protein. There is a program for such "inverse" motif recognition (which can be considered to be a 3D equivalent to ProSite motif matching !) in the SPASM suite (RIGOR), but its database is not of sufficient quality (generated by a simple program rather than a human structural biology expert) for it to be very useful at this stage.

Example of the result of a SPASM search. In this case, a seemingly unusual interaction between a Trp and a Met was observed in the interface of the complex between acetylcholinesterase and the snake venom toxin fasciculin. Thanks to SPASM, it became clear that, although the interaction is rare, it is not unprecedented. (Harel et al., 1995)

In the original JMB paper, the following applications were foreseen:

USF Practical "3D Motif Recognition" - Gerard Kleywegt

Latest update at 6 February, 2006.