K2d home page

Welcome to the k2d home page. Here we offer you an algorithm for the estimation of the percentages of protein secondary structure from UV circular dichroism spectra using a Kohonen neural network with a 2-dimensional output layer. You can either use k2d via a web server or get the program and run it on your machine. Also, note that an update of the method is available at K2D2.

We have used a self-organising neural network to extract from a set of circular dichroism spectra ranging from 200 nm to 241 nm the secondary structure features present in the data.

This information is kept in a matrix result of hundred different trainings of the neural network. k2d use this pre-calculated data to give you the result upon your CD data. The run does not take more than a few seconds and provides you with an estimation of the percentages of helix, sheet and random structure of your protein.

k2d also gives the probable error in the estimation, based in the training procedure results.

The Server

You only need to submit 41 CD values ranging from 200 nm to 240 nm (given in deg cm^2 dmol^-1 multiplied by 0.001) and the server gives back the estimated percentages of helix, beta and rest of secondary structure of your protein plus an estimation of the accuracy of the prediction.

The Program

k2d is written in C. We offer the source code and the executable files for Unix, PC, and Mac OS (contributed by Drew Engelbrecht), together with a weight matrix file, an example file and the instructions for its use.

Instructions for k2d

See the instructions for k2d, as they are shown in the k2d.read.me file.

Get the program

Different versions are accessible from: ftp://ftp.bork.embl.de/pub/software/andrade

If you want the program for PC you can get a zip-compressed file (1080 Kb) containing:
- the source C code for PC,
- the executable k2d for PC,
- the weight matrix file (4136 Kb),
- the k2d.read.me file,
- the example CD file.
The name of this file is k2d.zip
If you want the Unix version you can get a file (compressed using compress and tar) (1395 Kb) containing:
- the source C code for Sun Sparcstation,
- the executable k2d for Sun Sparcstation,
- the weight matrix file (4136 Kb),
- the k2d.read.me file,
- the example CD file.
The name of this file is k2d.SUN.tar.Z
If you want the program for Mac OS get one of the following files:
- k2d.OSX.zip (1.01 Mb),
- k2d.OSX.sitx (471 Kb)
kindly produced and provided by Drew Engelbrecht (d r e w e @ b r a n d e i s . e d u)

Frequently Asked Questions about k2d

Cite us!

The followings publications are related to the k2d algorithm:

Andrade, M.A., P. Chacón, J.J. Merelo and F. Morán. 1993. Evaluation of secondary structure of proteins from UV circular dichroism using an unsupervised learning neural network. Prot. Eng. 6, 383-390 Medline
Merelo, J.J., M.A. Andrade, A. Prieto and F. Morán. 1994. Proteinotopic Feature Maps. Neurocomputing. 6, 443-454

Please send comments or suggestions to m a n d r a d e @ o h r i . c a

[Andrade Home]