Back to Recipes Homepage
recipe picture
Recipe: PDBReader 0.9
Created by LociOiling 2 1
5
Your rating: None Average: 5 (1 vote)

Profile

Name: PDBReader 0.9
ID: 103090
Created on: Sun, 06/09/2019 - 07:43
Updated on: Sun, 06/09/2019 - 07:43
Description:

PDBReader reads PDB header records, including SHEET, HELIX, and SSBOND. You must copy the header and paste it into the recipe. PDBReader attempts to adjust the residue numbers to match the current protein in Foldit. PDBReader optionally applies the PDB secondary structure to the current matching protein.



Best For


Comments

LociOiling's picture
User offline. Last seen 1 hour 44 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
reads PDB header, adjusts secondary structure if all goes well

PDBReader scans the header section of a good, old-fashioned FORTRAN-flavored PDB file. It's focused on the information in the SHEET, HELIX, and SSBOND records. It also uses the DBREF and SEQRES records.

Assuming you know a suitable PDB entry, go to the PDB at rcsb.org and search for it. For example, you might use 2WWV for "Revisiting Puzzle 52: Bacterial Energy".

When the PDB displays the match, go to the "Display Files" dropdown and select "PDB Format (Header)". The header info is displayed, usually in a new browser tab. Select and copy (control-a, control-c) the whole thing.

In the recipe, paste the header into the "PDB Info" box on the first screen. You also need to know the chain. It's often "A", but in the case of 2WWV, chain "D" matches the protein from puzzle 52.

When you click OK, PDBReader scans the PDB header and attempts to match it to the current protein. Assuming this is successful (no guarantee there), the recipe displays a screen containing the sheets and helixes in Lua table format, and as a familiar secondary structure string, as seen in "print protein", "SS Edit", and similar recipes. If the are disulfide bridges, the results are displayed in "Bridge Wiggle" format.

The table version of the secondary structure is just a direct translation of what's in the PDB. You can copy and paste this information into your own recipe.
The string version is probably more useful, and works with existing recipes.

If the PDB info matches the current protein, you can click "Apply" to apply the secondary structure.

PDBReader doesn't do anything with the disulfide information. That's up to you and Bridge Wiggle.

If PDBReader doesn't find that the specified chain is an exact match to the current protein, you can still wing it, specifying your own offset and length. You'll get back much the same info as for a match, but there is no option to apply the secondary structure.

This version has been tested on all 15 of the "Rosetta Decoy" revisiting puzzles, and also the "Bacterial Energy".

Adjusting the residue numbers in the PDB to what's in Foldit is not always straightforward. PDBReader uses several tricks to handle the difficult cases. These tricks may not work correctly in some cases.

PDBReader also treats the Foldit protein as a single chain, so it won't work for the "Insulin Mutant" revisiting puzzle or other (rare) multi-chain puzzles.

LociOiling's picture
User offline. Last seen 1 hour 44 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
Small oops noted, some notes, and a couple of footnotes.

In both the dialogs and the scriptlog output, the offsets between the Foldit protein and the PDB entry are described as "PDB residue - Foldit segment".

In fact, the calculation is the other way around, "Foldit segment - PDB residue". So if segment 1 in Foldit matches residue 10 in the PDB, the offset is -9. Negative offsets are probably the most common.

Sometimes the extra residues at the start of a sequence are an expression tag or some other artefact, and aren't considered part of the chain. Even with an initial non-zero offset, the Foldit protein can be magically aligned to the PDB protein. Taking the starting residue from the DBREF record is what makes it happen. So what looks like an offset of -9 can end being a zero offset.

On the reference front, the PDB-101 tutorial Primary Sequences and the PDB Format is helpful. Nothing prevents starting residue numbers at zero or a negative number in a PDB file.

The structure of the PDB records can be found at wwPDB.org as Atomic Coordinate Entry Format Version 3.3.

Want to try?
Add to Cookbook!
To download recipes to your cookbook, you need to have the game client running.
Parent

none

Children

none

Authors
Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons