Macromolecular Modeling Blog ™

This is the fourth post in the CAPRI series, summarizing the presentations of Paul Bates, Martin Zacharias, and Carlos Camacho, as provided by the speakers. More to appear in the continuation of the series.

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You know the drill… a collection of relevant titles from the recent literature, if you want to discuss any of these, or expand on them, we’ll be more than happy.

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This is the third post in the CAPRI series, summarizing the presentations of Jeffrey Gray, Zhiping Weng, and Miriam Eisenstein, as provided by the speakers. More to appear in the continuation of the series.
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A meeting for everyone that liked this post (17 Protein disorder prediction servers):

Dates: 4-6 October, 2010

Venue: Institut d’Estudis Catalans, Barcelona, Spain.

Registration deadline: July 15, 2010.

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Schrödinger announced several days ago that it has reached an agreement with the estate of the late Dr. Warren L. DeLano to continue the development, support, and sales of the PyMOL software package.

PyMOL is well known to all of us in the field and is perhaps the most widely used and loved molecular visualization tool. According to the announcement, prior to his unexpected passing Warren DeLano, had been working closely with Schrödinger for over a year, and in constant discussions concerning ways to progressively integrate the companies’ products. Warren’s wife said: “I know this is what Warren wanted for PyMOL’s future.”

Tom Stout added on the CCP4BB that Jason Vertrees that has been working closely with Warren for the past several years as a co-developer has agreed to join Schrödinger.

However, a quick search on twitter shows a range of feelings towards this acquizition:

• Schrodinger now owns PyMOL. Will PyMOL now die a excoriating, excruciating death?
• I love pymol. Any idea what this means for the project?
• Good news about PyMOL?

What do you think this means for PyMOL’s future ? Tell us in the comments.

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This is the first post in a series, summarizing the CAPRI (Critical Assessment of PRediction of Interactions) 4th Evaluation meeting. In this post I’ll try to give a more personal perspective of the experiment results, the state and trends of computational protein-protein docking and the vibes behind the scenes. The next posts in the series will shortly summarize select talks from the meeting, kindly provided by the speakers.

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NAR just published the new special “Database” issue for 2010. We collected 23 papers that might be of interest to structural biologists, modelers and other protein people.

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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:

* 100^th percentile is the best among structures of comparable resolution; 0^th 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:

• UAB Statement on Protein Data Bank Issues
• On making shit up – by Richard Grant
• Pubmed structure pages of the forged structures – by Steve Koch
• ccp4bb thread: “The importance of USING our validation tools” - compiled by Hari Jayaram