DEJAVU, a program in the Uppsala Software Factory package, will search a database of Secondary Structural Elements and give you a list of PDB files that score well against that database. You have extensive control over the searching criteria.
Below is an example of the output from DEJAVU run with the pyrococcus woesei TATA-binding protein.
Nr Entry PDB SSE RMSD SCORE Compound
==== ===== ==== ==== ===== ===== ========
1 110 1ais 12 1.21 1.08 tata-binding protein/transcription factor (ii)b/tata-box com -
2 371 1cdw 12 1.78 1.55 human tbp core domain complexed with dna - organism_scientific: homo
3 1750 1ytb 11 1.60 1.37 tata-box binding protein (ytbp) complexed with dna containin - baker
4 1671 1vok 9 1.73 1.55 arabidopsis thaliana tbp (dimer) - organism_scientific: arabidopsis t
5 442 1crk 8 4.07 3.49 mitochondrial creatine kinase - organism_scientific: gallus gallus; o
6 968 1kap 8 5.97 5.03 molecule: alkaline protease; chain: p; synonym: p. aeruginos - organi
7 1193 1nir 7 3.83 3.31 oxydized nitrite reductase from pseudomonas aeruginosa - organism_sci
8 971 1kb5 7 3.87 3.26 murine t-cell receptor variable domain/fab complex - organism_scienti
9 165 1aoq 7 3.92 3.36 cytochrome cd1 nitrite reductase with substrate and product - organis
10 734 1got 7 4.39 3.70 heterotrimeric complex of a gt-alpha/gi-alpha chimera and th -
11 1485 1sme 7 4.71 3.96 plasmepsin ii, a hemoglobin-degrading enzyme from plasmodium - organi
12 544 1eag 7 4.79 3.80 secreted aspartic proteinase (sap2) from candida albicans co - organi
13 1325 1pmi 7 5.14 4.40 human rantes - organism_scientific: candida albicans; organism_common
14 1195 1nld 7 5.40 4.46 fab fragment of a neutralizing antibody directed against an - organis
15 846 1hrn 7 5.46 4.27 renin complexed with polyhydroxymonoamide inhibitor bila 980 - human
16 1488 1smr 7 5.57 4.43 renin (e.c.3.4.23.15) complex with the inhibitor ch-66 - mouse (mus m
17 1661 1vjs 7 5.77 4.83 structure of alpha-amylase precursor - organism_scientific: bacillus
18 349 1cau 7 6.18 5.12 canavalin (jack bean 7s vicilin) - jack bean plant (canavalia ensifor
19 2096 4aah 7 6.22 5.17 methanol dehydrogenase from methylophilus w3a1 - organism_scientific:
20 1823 2bbk 7 6.32 5.39 methylamine dehydrogenase (madh) (e.c.1.4.99.3) - (paracoccus denitri
Return to Post-structure Analysis
Revised: Wednesday, 21-Oct-1998 16:52:11 EDT