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You are about to perform Ramachandran Domain Analysis. Thank you for coming.
If you make use of the software for your researches, please give credit by citing this software, its authors and references in the litterature with the same authors.
Feel free to ask us for any information or to tell us about problems you may encounter. You can contact us to the following adresses.
- Matthieu Tanty : matthieu.tanty@gmail.com
- Marc-Andre Delsuc : delsuc@igbmc.fr
However, you are not allowed to modify this program, to use a part of this program or to make modifications to this program.

RamaDA version : 1.10 Sep 20 2011

Reference

Modelling the Ramachandran plane allows the natural characterisation of proteins
Tanty Matthieu and Delsuc Marc-André
Although a wealth of information about proteins and amino-acids conformations is contained in the Protein DataBank (PDB), this data is not available naturally. The Ramachandran plot is a tailor-made tool to analyse all the conformations : those involved in helices and sheets but also in polyproline-II (PPII) helices, random-coil regions and so on. Moreover, the quality of structures may be assessed directly by drawing this plot.
We developed a new modeling of the Ramachandran plot composed of eight independant domains, each describing a particular conformation : R-helices, alpha-helices, L-helices, beta, gamma, zeta, PPII and PPII_R. These domains have been fitted by 2D gaussian distributions over a representative subset of the PDB. With this statistical approach, we designed a method and a program, RamaDA (download at the bottom of this page), which is able to detect precisely residue conformations in a protein and to calculate a z-score to validate the structure. It can also display right-handed helices, beta-sheets, PPII helices and random-coil regions. Furthermore, it allows the determination of important structural patterns such as EF-hands which can be found into the all PDB with an accuracy of 99%.
Moreover, the 2D gaussian model developped coupled with a Bayesian approach lead to the determination of the conformational domains a protein adopts from its chemical shifts. The program able to achieve this analysis, RamaDP, can be downloaded at the bottom of this page.

Prerequisites

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How to use this server

Conformation assignment

Search for your PDB file on your computer and give it a name without space (optional).
Then, click on "Start calculation" and wait for the page to refresh.
If you want to analyse an other file, you just need to click on the "previous" button of your web browser and do the previous steps again.
WARNING: the web version of RamaDA is not able to memorize all the results.

Search for pattern

If you already have a conformational consensus, you can search for it over the entire PDB (update every week)
Enter it and click on "Search" and wait for the page to refresh.
To write the consensus, you can use python regular expressions syntax :
. : anything can be found
[XY] : X and Y may be found in this position
X{n} : X can be found exactly n times in-a-row
X{n,m} : X can be found at least n times but not more than m times in-a-row
Moreover, "e" can replace "[BPe]".
Example : EF-hands are composed of 9 amino-acids surrounded by two helices, the pattern is H{6,}..HH[LQ]HLBeeH{7,}
As a reminder, you can find the letter code for each domain at the bottom of this page.

Download script RamaDA

Download the latest version of RamaDA here (compressed file)

Download PDB analysis

Download the latest version of the analysis of the whole PDB by RamaDA (updated every week) here (compressed file)

Pattern :