Predicting Protein-3D structures based on homologous sequence search

This server is dedicated to find homologous PDB sequences to a given query sequence. It uses a version of pdb that includes all the PDB entries (excluding the BRK_MOD sequences and sequences only containing 'X's). Sequences are compared to this database with PSI-BLAST (Altschul et al, Nucl. Acids Res., 1997), using an e-value cutoff of 0.001, and a maximum of five iterations.

Coiled coil, transmembrane regions and low complexity regions are automatically filtered out from the query sequence, using COILS (Lupas, Curr Opin Struct Biol, 1997), TMpred (Hoffman & Stoffel, Biol. Chem. Hoppe-Seyler, 1993) and SEG (Wootton & Federhen, Computers and Chemistry, 1993), respectively. A graphical overview is given for the matched regions between the query sequence and found hit sequences. Here is an example of what the search result looks like.

The accuracy of the prediction was estimated to be above 98% (Huynen et al, J. Mol. Biol. 1998, please see below for the citation), based on the results from a test set of 685 PDB sequences extracted with PDB-select (Hobohm & Sander, Protein Science, 1994) that have less than 25% identity to each other.

Please cite this paper:
Huynen, M., Doerks, T., Eisenhaber, F., Orengo, C., Sunyaev, S., Yuan, Y.P., & Bork, P., 1998.
Homology-based fold prediction for Mycoplasma genitalium proteins.
J. Mol. Biol. 280, 323-326.

Yuan@EMBL-Heidelberg.DE, Dec. 1997 & modified at 08.Apr.1998.