Re: [ccp4bb] homology modeling

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: homology modeling
From: "Francisco J {- dot -} Enguita" fenguita {- at -} ITQB {- dot -} UNL {- dot -} PT
Date: 2009-05-05

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Subject: Re: homology modeling
From: Peter Schmidtke pschmidtke {- at -} MMB {- dot -} PCB {- dot -} UB {- dot -} ES
Date: 2009-05-05

Subject: Re: homology modeling
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-05-05

Modeller is indeed an excellent program (so are some others) but,
without being an expert, I was told some time ago and I am still under
the impression, that homology modeling with 20% identity (and many
insertions and deletions as you point out) is a dark art. Being able
to suggest the identical fold with some threading algorithm, is likely
all you will be able to do. A homology based model might be too much
to ask.

A.

On May 5, 2009, at 11:39, Chen, Yu Wai wrote:

> I would recommend Modeller
> http://www.salilab.org/modeller/
>
> Wai
>> Suppose I have two proteins A and B, they are structurally
>> homologous,
>> however the sequence identity is only about 20%. A has crystal
>> structure available, so if I want to model protein B, what's the best
>> way to do it? I don't think I can just thread the sequence of B to A
>> structure because the number of residues are different and there
>> might
>> be gaps and insertions in the alignment. Any suggestions of good
>> programs?
>>
>
>
> --
> Yu Wai Chen, PhD........................................Lecturer
> King's College London, Randall Division +44-207-848-8206
> New Hunt's House, Guy's Campus, London SE1 1UL, U.K.

P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: homology modeling
From: "Francisco J {- dot -} Enguita" fenguita {- at -} ITQB {- dot -} UNL {- dot -} PT
Date: 2009-05-05

Next message:
Subject: Re: homology modeling
From: Peter Schmidtke pschmidtke {- at -} MMB {- dot -} PCB {- dot -} UB {- dot -} ES
Date: 2009-05-05