Subject: CCL:protein folding/sequence.

From: Anne <[email-masked]>
Date: Sun, 16 Jul 2000 10:50:29 +0200

Homology does not mean "amino acid  sequence similarity >20%" It is  
defined  in terms of functionality (cf. analogy). For a clear definition 
see Attwood, T. K. & Parry-Smith, D. J. (1999). Introduction to
bioinfomatics (Cell and Molecular biology Series), Addison
Wesley Longman Ltd., Harlow, England. 

Comparative modelling methods require more than  aligning protein 
sequences, constructing structural models against canonical quaternary,
tertiary and secondary structural element templates  or using  threading
methodologies and then minimisation. It is  increasingly  knowledge based,
requiring more information on protein domain  motions (normal mode
analysis), catalytic group analysis, protein-protein activation and
modification, expression and regulation.

For seminal papers perform  citation searches on the following
publications and look for reviews that have used or criticised: 

Chou & Fasman (1978).  Advances in Enzymology, 47,  45-148

 Godzik et al (1993). J Computer-aided molecular design, 7, 397-438

Jones et al (1992). Nature 358, 86-89

Luthy et al (1992). Nature 356, 83-85

Mosimann et al (1995).  Proteins 23, 301-317

Novotny et al (1988). Proteins 4, 19-30

good luck 

James Smith

> I hear that if two sequences have homology (biological sequence
> similarity)
> greater than 20%, then their 3-d structures will be almost identical.
> 
> Is this true? If so, can someone point me to some seminal papers
> discussing
> this...
> 
> Thanks in advance. I will summarize if enough interest is shown.
> 
> Best Wishes, Iraj.
> 

_________________________________________________________________________

 James Smith       The Drug Design Group         01123 331 987 (Office)
 St.John's College Department of Pharmacology    01223 331 740 (Fax) 
 Cambridge         University of Cambridge       07625 395 084 (Pager)
 CB2 1TP           CB2 1QJ                       [email-masked]
 United Kingdom    United Kingdom        http://www.cus.cam.ac.uk/~js252
_________________________________________________________________________

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