FiltRest3D allows to find 3D protein models which best match experimental restraints. It scales well and could be applied to hundreds of thousands of homology models or de novo decoys.
Processing of your data proceeds in three steps:
Restraint types available in the current version are:
If you have just few models, you can upload PDB files directly:
If you have many decoys, it is advised to pack your PDB files into .ZIP file,
bash$ zip /tmp/PVI.zip PvuII/*.pdb
and download whole file. Then one may use pre-filled form with restraints to see the results.
Distance restraints may be for example derived from crosslinking experiments. Let us assume 22 Å long cross-linking agent, so we assume that C-β atoms of bound residues are at most 24 Å apart. Below is an example restraint between surface lysines 78 and 118.
If experimental evidence for particular restraint is weak and uncertain, it is possible to assign a weight <1 to this restraint with a weight field. When particular restraint is strongly supported by experiments (like active center of the protein with a known biochemical function), the restraint weight above 1 may be used.
Partial knowledge of secondary structure motifs can be entered using secondary structure restraints. Below is simple restraint preferring models with β-strand from 18th to 24th residue.
Assuming that aminoacid is known to be on a protein surface, we can use crude relative solvent accessibility estimation above 30% for a residue 67 that we believe is fully exposed or below 5% for a residue 98 that is fully buried.
As far as it is known today, real protein structures do not have topological knots except for one protein family, but it is common for modelling programs to produce such knotted models. This option is time consuming but allows to eliminate all these knotted protein models.
After ranking the data you are given output like the screenshot below.
The most important is the table of all decoys with filename in the first column and
total score in the second. Following columns contain decomposition of scores to individual restraints.
When restraint is satisfied, then the score is 0.0, when it is completely violated
(or cannot be checked because of incomplete data), the value of 100.0 is assigned.
To facilitate error-checking, the web server also includes full copy of standard output
and standard error streams from FiltRest3D engine.
Standard output contains the table of results in Comma Separated Values
format with colon ':' used as a record separator.
It can be easily parsed or imported into spreadsheet.
Standard error contains all errors and warnings, including these which cause assignment
of maximum ranking penalties because of missing data.
Developed by Marta Kaczor, Anastasia Yu. Bakulina and Michał J. Gajda<mgajda@genesilico.pl>
Currently maintained by Michal J. Gajda <mgajda@genesilico.pl>.