How to use this database

(1) Choose the search tab

(2) You can use simple search, advanced search or submit a protein structure.

(2.1) Simple search option:

Using this option you can search in the database for one or several PDB(s) files using 4 letters PDB code, e.g., 7ODC, you can also add the PDB chain, e.g., 7ODCA. You are free to use upper case or lowercase letters for PDB code.

You can also submit several PDB code at one time, separated by space or comma.
Example: 7ODCA 1atn 1akk 1KOKO 3bog 2bpE

(2.1.1) A new page is generated

On this page, you have access to the list of submitted PDB ids. 50 PDBs can be displayed on the same time.

(2.1.2) Some PDBs can not be already present and analysed in PolyprOnline database.

In this case, you can decide to submit this PDB to PolyprOnline database: system is able to automatically download and analyse them. Nonetheless, these actions take more time to treat. Be careful to submit one PDB file after another.
Here differents cases are presented:

- Submit 1AKK

A message appears:

Then if computation is succesful a new message is displayed:

- Submit 1KOKO

This PDB code does not exist, a message is printed:

- Submit 3BOG

There is a 4 chains in this PDB file, it takes times to treat them. At the end the result is displayed:

- Submit 4BPE

It's a very large PDB file with an important number of chains. The PDB must be split by chains it requires too many computation times to treat it at a whole. It is necessary to submit each chain separately e.g., 4BPEA, 4BPEB etc.

At the end the pages look like:

(2.1.3) To access to detailed analysis and assignment of protein structure in term of secondary structures you must click on PDB code

Go to section (3).

2.2) Advanced search

In advanced search mode you are able to perform more complex query. You can perform a query to retrieve structures in the database by resolution (Å), protein length, minimal number of residues in PPII conformation, pattern of secondary structure.
The advanced search database contains 24,761 protein chains extracted from a list of non reduntant set culled PDB by PISCES* (only X-Ray structures, maximum of 90% sequence identity between each protein chains, resolution less than 3.0 Å).
*Reference: G. Wang and R. L. Dunbrack, Jr. PISCES: a protein sequence culling server. Bioinformatics, 19:1589-1591, 2003.

2.2.1) Choice of methods for number of residues in PPII conformation and pattern search

2.2.2) Minimal number of residues in PPII conformation in protein

2.2.3) Pattern of secondary structure

You can search a fragment of specified conformation contained in a given structure using a simple regular expression pattern. Pattern search uses the following rules:
- Direct use of conformation code Letters (detailled in section (3.1.1) )
Example: HHHH-PPEEE

- You can introduce special character:
X means any of conformation. Example: PPXXXPP

- You can specify minimal and maximal length of conformation:
{1}exactly one given conformation
{1,3}one to three given conformation
Example:
PPPX{2,4}PP
H{7}-{1,4}E{3,5}
- You can introduce "jokers"
* : 0 to n any conformations
Example:P*P
These conformations can be retrieved PP PPP PPPP PP---PP...

(3) To access to detailed analysis and assignment of protein structure in term of secondary structures you must click on PDB code

A new page appear:

On this page different analysis are displayed

(3.1) Analysis of secondary structures using 4 different secondary structure assignment methods

Alignment on different assignments
One code letters is used to represent specific conformation. Letters are colored accordingly to more generals class of secondary structure (e.g., helix residue in red, strand in green, polyproline II helix in blue and non regular secondary structure in grey).
Letter codes correspond to:

(3.1.1)DSSP PPII:

H - 4-turn helix (α helix). Min length 4 residues
G - 3-turn helix (310 helix). Min length 3 residues
I - 5-turn helix (π helix). Min length 5 residues
T - hydrogen bonded turn (3, 4 or 5 turn)
E - extended strand in parallel and/or anti-parallel β-sheet conformation. Min length 2 residues
B - residue in isolated β-bridge (single pair β-sheet hydrogen bond formation)
S - bend (it is a non-hydrogen-bond based assignment)
"-" - coil (residues which are not in any of the above conformations)
P - Polyproline II helix (in Mansiaux et al.)

References:
Kabsch W, Sander C Biopolymers 22: 2577–2637 (1983)
Mansiaux Y, Joseph AP, Gelly J-C, de Brevern AG PLoS One 6 (3):e18401 (2011)

(3.1.2)PROSS:

H - α helix
T - β turn
E - β strand
P - polyproline II
C - coil

Reference: Srinivasan R, Rose GD Proc Natl Acad Sci USA 96, 14258–14263 (1999)

(3.1.3) SEGNO:

e and E - Strand
p and P - Polyproline II
H - alpha Helix
g and G - 3-10 Helix
I - Pi helix
O - Coil (coded as "-" in this webserver)
b and B - Isolated Strand

Reference: Cubellis MV, Cailliez F, Lovell SC BMC Bioinformatics 6, Suppl 4S8 (2005)

(3.1.4) XTLSSTR:

H and h - Alpha helix
G and g - 3^10 helix
E and e - Extended beta strand
T - Hydrogen-bonded
N - Nonhydrogen-bonded (N)
P and p - Beta-turns, and polyproline II type (3-1) helix

Reference: King SM, Johnson WC Proteins 35, 313–320 (1999)

(3.2) Download data

You can donwload analysed data for your own usage.

(3.3) Jmol Applet

You must click to display the full 3D vizualisation using a Jmol applet (Reference: Jmol: an open-source Java viewer for chemical structures in 3D. https://www.jmol.org/)

You are able to visualize different assignment dynamically on 3D structure representations (Cα trace only, cartoon)
Local conformation are colored with same color scheme used for the 1D alignment (see section 3.1)

(3.4) Ramachandran Plots

Ramachandran plots give the distribution of φ and ψ torsion angles for each used methods. The most frequent areas for α-helix and β-sheet are shown in the background of the plot (represented by a color scale). Statistics about areas were derived from our previous study. Residues assigned as PPIIs are represented as white point. The image is mouse sensitive and gives additional information on residue number, nature and phi and psi angle value that is pointed at.

Hover mouse on point to display precise value and information.

You can also click on the image to display a largest version.