The MetaPSICOV tool for precise structural contact prediction

Current contributors: David T. Jones, Tanya Singh, Tomasz Kosciolek, Stuart Tetchner

For queries regarding MetaPSICOV: email and include 'MetaPSICOV' in the subject.

INPUT - Single amino acidic sequence in FASTA format

Any valid amino acidic sequence can be inserted here:

To test the services of MetaPSICOV follow this link to retrieve a test fasta sequence. The test set of MetaPSICOV is available here

Please enter a short name for your sequence.

Please enter the e-mail address to which results should be sent.

Using MetaPSICOV

In order to use MetaPSICOV, click on the 'Main Input' tab and fill the form, according to the following instructions.

Firstly, please enter a protein sequence (one amino acidic sequence only, in FASTA format)

A short identifier is needed to label your submission - please keep it short and simple. Moreover, if you indicate your email address you will receive an automated email as soon as your job has completed, containing a link to the appropriate result page (this is not required, but highly recommended).
At the bottom of the form you will find the button for submitting your job, together with the button you can use to reset the form.

MetaPSICOV is an algorithm incorporating different approaches of contact predictions implemented with a neural network in order to improve the accuracies of the predicted contacts. The web server takes amino acid sequence in fasta format and outputs the precision scores of the predicted contacts for MetaPSICOV stage 1, MetaPSICOV stage2 and MetaPSICOV-hb. The results for MetaPSICOV stage 1 and MetaPSICOV stage2 are in the following format:

58 65 0 8 0.999999
59 64 0 8 0.999989
23 28 0 8 0.999152
5 28 0 8 0.995360
6 33 0 8 0.993700
57 66 0 8 0.992729
6 31 0 8 0.987090

where the first two columns represents the residue number and the last column represents the precision values. In the third column, 8 represents distance between these two residues. The two residues are considered to be in contact if the Cβ-Cβ distance is below 8 Angstrom, which is accordance with the standard assessment procedure introduced in the Critical Assessment of protein Structure Prediction (CASP) experiment.

A contact map corresponding to MetaPSICOV stage 1 is given as an ouput in the form of a png file.

For MetaPSICOV-hb the first column represents the hydrogen bond donor and the second column represents the hydrogen bond acceptor. The third column 3.5 represents the residue distance and the last column represents the probablity.
If you use this program, please cite :

Jones, D.T., Singh, T., Kosciolek, T., Tetchner, S. MetaPSICOV: Combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinformatics Advance Access published November 26, 2014. [Reprint]

Jones, D.T., Buchan, D.W., Cozzetto, D. & Pontil, M. (2012) PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics. 28, 184-190. [Reprint]