Homology-modelling HEXA

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Revision as of 11:54, 7 June 2011 by Link (talk | contribs) (Methods)

Homology structure groups

We decided to choose every 5% one protein:

> 60% sequence identity
PDB id name similarity single template
1ht6_A AMY1, alpha-amylase iso 95%
3aj7_A Oligo-1,6-glucosidase 90% X
1h4p_A Glucan 1,3-beta-glucosidase 85.2%
3bc9_A AMYB, alpha amylase, ca 80.8%
2zum_A 458AA long hypothetical 75%
3bmv_A Cyclomaltodextrin gluca 70.3%
2f2h_A Putative family 31 gluc 64.8%
3emz_A Xylanase, endo-1,4-beta 61% X
> 40%
2dep_A Xylanase B, thermostabl 54.9%
3cui_A EXO-beta-1,4-glucanase; 49.5%
1vhc_A Putative KHG/KDPG aldol 45.1%
2hk0_A D-psicose 3-epimerase 40.8%
< 40%
2g0w_A LMO2234 protein; putati 35.5%
3q94_A Fructose-bisphosphate a 30.0%
3hn3_A Beta-G1, beta-glucuroni 25.1%
3lut_A Voltage-gated potassium 20.1%




First of all we need a pairwise alignment. Therefore, we used the Needleman-Wunsch Algorithm implemented by EMBOSS http://www.ebi.ac.uk/Tools/psa/emboss_needle/. We used the standard parameter.