Dear Consortium Members and Affiliates,
As July comes to a close we have a brief update on SBGrid news, with a recently posted software tutorial on YouTube, a new Schrödinger tool for many of our members to try, a story on Alejandro Buschiazzo's Uruguayan lab, updates to our software collection, a welcome to five new members, and highlights from three member publications.
This week's webinar featured the molecular biology suite, Geneious with Christian Olsen presenting - watch on SBGridTV. We'll take a break from webinars in August, but will resume in September with Schrödinger's Daniel Cappel presenting on PyMOL.
Our Schrödinger working group will also resume in September with a demonstration of their new Protein-Ligand Database (PLDB). With the renewal of our license for North American labs, Schrödinger included a limited number of licenses for this tool, which is described as a knowledge base of 3D structural data and protein-ligand interactions for idea generation and validation. PLDB product manager Ishita Aloni will present. If you'd like to get started using PLDB now, please email email@example.com for login credentials. See the PLDB flyer for more information.
July's SBGrid WebTale focuses on Alejandro Buschiazzo, who heads up our first member laboratory in South America at the Institut Pasteur, Montevideo in Uruguay. Buschiazzo made the leap from Paris to Montevideo in 2006 to build an X-ray crystallography core that now serves labs from many neighboring countries. He is also responsible for establishing and maintaining one of three Data Access Alliance centers that act as mirror sites for SBGrid's Structural Biology Data Grid.
We pushed out a small software release in July. You'll see updates to ATSAS, CCP4, knuspr, Schrödinger, and xdsme. We also added ICM-Browser-Pro to the collection and hope that you'll give us feedback on this new software tool.
July also brought us 5 new members: Jack Dunkle from the University of Alabama, Dhirendra Simanshu from Frederick National Lab, Vatsan Raman at the University of Wisconsin-Madison, Haribabu Arthanari at Dana-Farber Cancer Insitute, and Christopher Lemke from the Broad Institute. Welcome to our new members!
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data in the Structural Biology Data Grid along with the PDB record deposit and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
SBGrid received 3 new citations in member publications in July: Gil Privé from U Toronto gave us a nod in his J Mol Biol article on Human Acid Sphingomyelinase, Sliz lab alumnus Yunsun Nam of UTSW acknowledged SBGrid in her Mol Cell publication on Mettl3 and Mettl14 Methyltransferases, and Thomas Brett cited us in his article on MAPK13 inhibitors appearing in Biochim Biophys Acta.
Over 60 publications from SBGrid member laboratories have appeared in journals since our last newsletter. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- In a Nature article from the laboratory of Robert Lefkowitz at Duke University we learn that G-protein-coupled receptors have a scope of influence much greater than previously understood. Nature. 2016. 535:448-52.
- A new Preview from Allan Drummond's group at the University of Chicago that appeared in Molecular Cell does a round up of recent studies on Heat Shock Factor 1 that redefines its roll in the heat shock response, giving it the new title of crowd-control manager. Mol Cell. 2016 ;63:1-2.
- From our undergraduate desk: Harvard student Kristen Rodrigues highlighted a story in Nature Communications from Richard Cerione's lab at Cornell that offers new insight on the communication happening inside blastocyst cells to encourage implantation. Read more on Tumblr.
ATSAS version 2.7.2-5 is the new default.
CCP4 version 7.0.015 was pushed out. This version introduces a new modularized version of AMPLE, a new glycan viewer in ccp4mg, reworked stereochemistry detection in privateer, and a number of other improvements.
ICM-Browser-Pro version 3.8.4 is new to SBGrid. ICM-Browser-Pro is a high quality visualizer and annotator for three dimensional molecular structures, sequences, alignments, chemical spreadsheets, and biological data.
knuspr was updated to version 20160713 (Mac only).
With the Schrödinger 2016-2 release, you can give the beta version of Maestro 11 a whirl while enjoying some usability and performance enhancements overall. Schrödinger would like your feedback on this beta version.
xdsme was updated to version 20160406.
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.