| Quick navigation: | Home | Site Map || References | Biography || Copyright | Other copyright | Contact us | Advert | | |
Re: [ccp4bb] Judging a homology model |
||
- Protein crystallographyMain steps:- Protein purification- Crystallisation Special:- Programs for crystallography- X-ray detectors Basic tutorials:- Chemistry- Protein - Peptide - Amino Acids Xtal community:- CCP4BB |
CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Judging a homology model From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE Date: 2010-01-06 >> Dear Friends, >> >> I have a question about judging a homology >> model. I have three homologous proteins A, B and C of which only A has >> 3D crystal structure available. Their similarities/identities are >> given below. >> >> Pair-wise alignment similarity/identity (%) >> >> A and B 63/49 >> >> A and C 54/39 >> >> B and C 60/46 >> >> Assuming all the above data are right, which of the following way >> would give the best model for C? >> >> 1. Building homology model of C with A as template. >> >> 2. Building homology model of B with A as template and then use B >> as template to build C. >> >> Suppose I used MODELLER for this work where an energy minimization >> step is involved after threading the query sequence on the template. >> >> I need to know which model for C will be better and why? >> >> Thanks for your answer… >> >> Happy New Year to you all, >> >> Raja Raja, you should take the alignment of B to A into account when you establish the alignment of C to A. In other words, construct a multiple alignment first (and use sequences D, E, ... as well if they exist), and only then build your homology model. The reason is that the biggest source of error in a homology model comes from misalignment of the target and the model sequence. You want to avoid this. HTH, Kay CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
|
| ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd |