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Eight examples of ProSMoS results
To illustrate ProSMoS performance, we carried out searches for eight common structure patterns. The eight structure patterns are those defined on the TOPS web site and they are the most common structure patterns in protein fold space. When constructing the query matrices of those eight structure patterns, we followed the standard definition of corresponding fold by referring SCOP and looking representative structure manually. The target database is our meta-matrices database constructed on full PDB. If you want to look at the result of searching against SCOP40, please refer here
1. Beta Grasp (Ubiquitin like fold)
2. Greek Key
4. Jellyroll
5. Keyroll
6. Plait (Ferredoxin like fold)
8. Tim Barrel
Beta grasp fold, i.e. ubiquitin-like fold, has a two-layer alpha+beta architecture with a alpha-beta-beta-alpha-beta-beta core, in which four beta-strands form a mixed beta-sheet with a strand order 2143. Strands 1 and 4 are parallel and an alpha-helix connects strands 2 and 3 to form a right-handed beta-alpha-beta unit.
We define the query matrix for beta grasp fold like below:
1 2 3 4 5
E E H E E
* t C - c
* T - -
* x C
* t
*
handedness 2 3 4 R
length 3 H 8 1000
Want to see the results of beta grasp pattern search? Please click here
Greek key is a popular decorative repeating unit used in Greek art and Roman art. In structure biology, Greek Key motif occurs frequently in anti-parallel beta structures providing a simple way to connect anti-parallel beta strands that are on opposite sides of a barrel structure.
We define the query marix for green key like below:
1 2 3 4 5
E E E E E
* - - t -
* t - t
* t -
* -
*
sheetS 1 2 3 4 5
Want to see the results of greek key pattern search? Please click here
Immunoglobulin fold is one of the most well studied structure fold type. It forms a sandwich structure with two anti-parallel beta sheets packed tightly against each other. Normal Immunoglobulin structure usually contains 8 strands.
We define the query matrix for immunoglobulin as below:
1 2 3 4 5 6 7 8
E E E E E E E E
* t X X - - X X
* X X - t X X
* t X X t -
* X X - -
* t X X
* X X
* t
*
sheetS 1 2 5 6
sheetS 3 4 7 8
sheetD 1 4
sheetD 5 8
handedness 1 2 3 R
handedness 2 3 4 R
handedness 3 4 6 L
handedness 3 5 6 L
handedness 5 6 7 R
handedness 6 7 8 R
handedness 6 7 1 R
handedness 7 1 2 L
handedness 8 2 3 R
Want to see the results of immunoglobulin pattern search? Please click here
Jelly roll usually strands for a protein structure consisting of cylindrically-arranged Greek key motifs with inter-strand connections running alongside the termini of the cylinder to produce a closed structure. Its shape is superficially similar to a capped beta-barrel and also to a Swiss jelly-filled roll, hence the name.
We define the query matrix for jelly roll as below:
1 2 3 4 5 6 7 8 9 10
E E E E E E E E E E
* t X - X X - X - X
* X - X X - X t X
* X - - X t X t
* X X t X t X
* t X t X -
* X - X -
* X - X
*
X -
* X
*
handedness 1 2 3 R
handedness 2 3 4 R
handedness 3 4 5 R
handedness 4 5 6 R
handedness 5 6 7 L
handedness 6 7 8 R
handedness 7 8 9 R
handedness 8 9 10 R
handedness 9 10 1 R
handedness 10 1 2 L
sheetS 1 2 4 7 9
sheetS 3 8 5 6 10
sheetD 1 10
sheetD 6 7
Want to see the results of jelly roll pattern search? Please click here
It forms a barrel structure which is similar with jelly roll to some extend.
We define the query matrix for Key roll as below:
1 2 3 4 5 6
E E E E E E
* t X X X t
* X X t X
* t X t
* t X
* X
*
sheetS 1 2 3 4 5 6
handedness 1 2 3 R
handedness 2 3 4 R
handedness 3 4 5 L
handedness 4 5 6 R
handedness 5 6 1 R
handedness 6 1 2 L
Want to see the results of key roll pattern search? Please click here
Plait also called as ferrodoxin-like fold which is a common alpha+betal structure with the SSEs order αββαβ and its two terminal beta-strand hydrogen-bond to the central two beta-strands, forming a four-stranded, antiparallel beta sheet covered on one side by two α-helices.
We define the query matrix for Plait as below:
1 2 3 4 5 6
E H E E H E
* X - t C t
* X C X X
* t X -
* X -
* X
*
handedness 1 2 3 R
handedness 2 3 4 L
handedness 3 4 5 R
handedness 4 5 6 R
handedness 5 6 1 L
handedness 6 1 2 R
handedness 1 2 5 L
sheetS 1 3 4 6
Want to see the results of plait (ferredoxin) pattern search? Please click here
Rossmann fold is very popular in protein universe. It is the major fold type used in alph/beta structure class. Rossmann fold is discovered by Prof. Michael Rossman in the lactate dehydrogenase protein in 1970.
Rossmann fold is a 3 layer, alpha-beta-alpha structure with parallel beta sheet in the middle linked by alpha helix. The starting strand extending on one side by the unit of beta-alpah-beta and then through a cross over, the chain folded back on the other side of the starting strand and the first secondary structur element after crossover is a strand H-bonded with the starting beta strand.
We define the query matrix for Rossmann fold as below:
1 2 3 4 5 6 7 8 9
E H E H E H E H E
* T c X - T c X -
* X X X X X X X
* T c X - X -
* X X X X X
* X - X -
* X X X
* T c
*
X
*
sheetS 1 3 5 7 9
handedness 1 2 3 R
handedness 2 3 4 R
handedness 3 4 5 R
handedness 4 5 6 L
handedness 5 6 7 R
handedness 6 7 8 R
handedness 7 8 9 R
handedness 1 2 9 L
handedness 1 6 7 R
Want to see the results of rossmann fold pattern search? Please click here
Tim barrel is one of the most famous structure fold type. In the barrel, the alpha helices connect the parallel beta strands outside of the barrel. Typically, there are eight strands and eight helix in Tim barrel.
We define the query matrix for Tim barrel as below:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
E H E H E H E H E H E H E H E H
* T c X X X X X X X X X X X c X
* T X X X X X X X X X X X X X
* T c X X X X X X X X X X X
* T X X X X X X X X X X X
* T c X X X X X X X X X
* T X X X X X X X X X
* T c X X X X X X X
* T X X X X X X X
* T c X X X X X
* T X X X X X
* T c X X X
* T X X X
* T c X
* T X
* T
*
handedness 1 2 3 R
handedness 3 4 5 R
handedness 5 6 7 R
handedness 7 8 9 R
handedness 9 10 11 R
handedness 11 12 13 R
handedness 13 14 15 R
handedness 15 16 1 R
sheetS 1 3 5 7 9 11 13 15
Want to see the results of tim barrel pattern search? Please click here