[BiO BB] (no subject)

[Iddo Friedberg]

Hi Pankaj,

Threaders can predict folds for a larger chunk of sequences than, say,
homology modelling, but they cannot place "any sequence onto any
structure" because:
1) We do not know all the strucutres.
2) The energy functions are not 100% specific and sensitive. Errors do
occur.

I guess what you would really like is a good strucutre prediction program.
I would start with a web-based metaserver. The metaservers incorporate
information form different structure prediction programs, and thus
sometimes achieve better results than one specific program. You can then
look into the results of the individual programs, decide what you like,
and in many cases download it for standalone running.

One such metaserver is:
http://bioinfo.pl/Meta/

The quality of the individual servders is evaluated here:
http://bioinfo.pl/LiveBench/

With links to the server sites.

I hope this helped,

Iddo

--
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037, USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://ffas.ljcrf.edu/~iddo

On Sun, 1 Feb 2004, Pankaj wrote:

> hi all,
> i have a set of sequences whose similarity among themselves is very
> poor. i want to have a good threading program which can thread these
> sequences on a known structure (as i know that all of them take the
> same fold). 
> i have read somewhere that threading programs can thread any sequence
> onto any strcuture...in that case how do i make sure that the
> threading result is right?
> please suggest me some good threading programs which can be downloaded
> and run locally on the computer.
> thanks in advance
> pankaj
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