2ndry structure prediction

Nicolas Le Novere nl223 at cus.cam.ac.uk
Wed Apr 5 03:43:16 EST 2000

"Richard P. Grant" wrote:

> Please excuse the x-post.  Which secondary structure prediction method
> is generally reckoned the 'best' these days.  I know about
> http://www.EMBL-Heidelberg.DE/predictprotein/  would appreciate any
> other pointers.

see http://www.pasteur.fr/recherche/unites/neubiomol/ secstrpr.html
for pointers, references and a little discussion.

Important: use SEVERAL programs, based on DIFFERENT approaches 
See the result of JPRED with PHD+DSC+NNSSP+PREDATOR

Currently the best are:

->statistical information (GOR, hydrophobicity etc ...)
	DSC - It is not maintained anymore, because its son, PROF
is launched. However nothing is published. You can find DSC on the
pasteur website. Q3 ~ 70-72

->nearest-neighbor (~similarity with protein of know structures)
	NNSSP    Q3 ~ 68-72

	PSIPRED - it is a sort of reimplementation of PHD, with a 
currated alignment as input, and a better training. Q3 up to 76%

	SAM99, aimed to be a fold-recognition program, can provide
good secondary structure predictions.

Dr Nicolas Le Novère                   e-mail: nl223 at cus.cam.ac.uk 
Dpt Zoology, Univ Cambridge, Downing street, Cambridge CB2 3EJ, UK

tel: +44 1223 336623                          fax: +44 1223 336676

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