Help



1. Summary


The PconsFold2 pipeline uses contact predictions from PconsC3, the CONFOLD folding algorithm and model quality estimations to predict the structure of proteins. Here we show the result of applying PconsFold2 to Pfam families, both with and without known structures.



2. Usage


The main site shows a list of all Pfam families and whether they have a generated model or known structure. The table can be sorted and filtered by the search bar. Click on a family of interest to see details.



3. Output


For each family a set of models has been predicted with the PconsFold2 pipeline. These models are ranked by model quality assessment. These model quality assessment scores further provide the basis for an estimate on the trustworhtiness of each model. This is especially helpful for families that do not have a known structure. The top ranked model is shown in the detail pages along with its predicted contacts. See PconsFold2 for more details.

Length

Length of the representative sequence of the PFAM family.

Meff

Number of effective sequences as described by Ekeberg et al.,2013. This is calculated from the alignments run by HHblits and Jackhmmer from the representative sequences for each family. The Pfam alignments were ignored.

FDR

False Discovery Rate, the expected proportion of type I errors.



4. References


PConsfold2: Pfam data
Michel M, Lamb J, Elofsson A

Large-scale structure prediction by improved contact predictions and model quality assessment.
Michel M, Menéndez Hurtado D, Uziela K, Elofsson A



5. Contact


Arne Elofsson group

Department for Biochemistry and Biophysics
The Arrhenius Laboratories for Natural Sciences
Stockholm University
SE-106 91 Stockholm, Sweden

Science for Life Laboratory
Box 1031, 17121 Solna, Sweden

E-mail:   arne@bioinfo.se
Phone:   (+46)-8-16 4672
Fax:   (+46)-8-15 3679