1000 down, few more thousands to go

Congratulations, the SGC (Structural Genomics Consortium) just released the 1000th high resolution protein structure!

The 1000th structure – PDB ID 2xml – belongs to JmjD2C, a protein involved in epigenetic signalling. JmjD2C is known to play a key a role in the maintenance of self renewal in stem cells as well as roles in cancer.

1000'th structure solved by the SGC

I'm the 1000'th structure solved by the SGC. PDB id 2XML

B.t.w. the news release by the welcome trust received intense coverage by science news websites and blogs (mostly reposting, e.g. Genetic Engineering and BioTech News,The Medical News, Biology News Net,Red Orbit,Science Daily &

Written by Nir London in: News | Tags: , , ,

PDB mode for Emacs

Are you tired of manually editing PDB files ?

Checkout this PDB mode for Emacs that helps you do most of the usual modeler editing tasks in a press of a button.

Via @leninwtigger

Written by Nir London in: Resources | Tags: ,

How to detect a forged PDB

Most of you probably heard about the recent retraction of some 12 structures (1BEF, 1CMW, 1DF9/2QID, 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0) from the PDB. Reported first by The University of Alabama at Birmingham and follwing by structural biology blogs as p212121 and ByteSizeBio – also known as “Structuregate”. One question that arises is – was this preventable?

Soon after the issue was published, Gerard Kleywegt has posted an oficial statement on behalf of the wwPDB on the Retraction of “UAB PDB entries”, stating the pdb official policy and noting that:

wwPDB has convened expert, community-driven Validation Task Forces for X-ray (in 2008) and NMR (in 2009) to advise on the most suitable criteria to use for validating structure entries (model, data and fit of model to data) when they are deposited. The recommendations of these task forces will be implemented as part of the deposition and annotation procedures of the wwPDB partners.

To see if these procedures would have discovered the culprit we used the PDB Auto Deposit Input Tool (ADIT) validation, which as it seems run the PROCHECK and MolProbity software on the deposited structure. The results were quite convinving! Below is a table summaryzing MolProbity’s results on the structure 1BEF which was the first to be retracted:

Clashscore, all atoms: 110.32 0th percentile* (N=576, 2.10Å ± 0.25Å)
Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.
Poor rotamers 18.57% Goal: <1%
Ramachandran outliers 2.86% Goal: <0.2%
Ramachandran favored 89.14% Goal: >98%
C? deviations >0.25Å 1 Goal: 0
MolProbity score^ 4.04 1st percentile* (N=11758, 2.10Å ± 0.25Å)
Residues with bad bonds: 0.00% Goal: 0%
Residues with bad angles: 0.00% Goal: <0.1%

* 100th percentile is the best among structures of comparable resolution; 0th percentile is the worst.

RosettaHoles, by Will Sheffler is a Rosetta protocol designed to asses protein core packing, originally designed to select succesfull protein designs but was shown to be usefull for structural validation. In the paper published a year ago, RosettaHoles was tested against the entire PDB and detected 7 out of the 12 retracted structures as outliers.

What other validation tools would have done the work? Another question that might be interesting is, starting with the (apperantly) falsified coordinates could molecular modeling reconstruct the correct sturcture? Could at some point modeling serve as the validation itself ?

Some more reading and resources on this issue:


PDB Widgets

As from next week, the RCSB PDB will provide web widgets – small bits of code, which provide PDB functionality that you can embed in your own website. All of the widgets that are provided are 100% self contained JavaScript files and will be maintained by the RSCB PDB. We’ve taken some of those widgets for a test drive.


Written by Nir London in: Resources | Tags: , , , , ,

The Europeans are cleaning up the PDB, woohoo!!!

I just read this summary from Katharine Sanderson in Nature about an effort led by Gert Vriend to correct and improve crystallographic structures in the PDB. I’m going to read their paper, “PDB_REDO: automated re-refinement of X-ray structure models in the PDB” before I get too excited about it, but Ms. Sanderson said the R-free’s are going down, so my hopes are high.

Correcting errors in structures in the PDB in an automated fashion has been sorely needed for a long time. When it comes to modeling, benchmarking, and experimentation based on structures from the PDB, GIGO.

Written by Xavier Ambroggio in: Literature Reviews | Tags: , , ,

Short Course: Crystallography for Modelers

The RCSB PDB will host a short course for practicing modelers looking for a better understanding of crystal structures and PDB data.

Dates: May 7 & 8 at Rutgers, The State University of New Jersey in Piscataway, NJ.

The target audience is PDB data users working in pharmaceuticals, biologicals, chemical industries, academia, and others who are looking to understand how to interpret in crystal structure data: possible problems, errors, and accuracy; how the data is determined and annotated; and what information and data is provided beyond atomic coordinates.

To learn more and register: Crystallography for Modelers

Written by Nir London in: Events | Tags: , , , , ,

Molecules on the go – iPhone app.

How many times have you talked to someone at a conference, or in a meeting and tried to explain to him, while hand waiving or napkin drawing, that cool structural feature of your protein? Well, with “Molecules” the hand waving can stop and the finger waving begins.


Written by Nir London in: Resources | Tags: , , , ,

Weird PDB statistics

A list of Useful, Useless or simply Interesting facts on Proteins, Structures and what’s around them, generated by OCA: a browser and database for structure and function. Adopted from Proteopedia.


Written by Nir London in: Weird science | Tags: , , , ,

PDB fetcher Google Gadget

Have you ever read a paper, stumbled upon some random PDB id and was itching to see the structure ? maybe play with it for several minutes ? get a general impression ? but, alas, you were too lazy to actually go the PDB and download the structure! Carson Andorf provides an easy solution in the form of a “PDB Structure Viewer with Sting!” Google Gadget. 

Just enter your PDB id and viola you get an image of the structure another click on the image would let you play around with it. Add this to your iGoogle page and you’ll never shun another molecule again. And while your at it, add the macromolecular modeling blog feed to your iGoogle page as well Add to Google  :)

What is your favorite google gadget ? Tell us in the comments.
Easy to use google gadget to view PDBs

Written by Nir London in: Resources | Tags: , , , , , ,

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