Dear Consortium Members and Affiliates,
With June and the lure of summer on our doorstep we have news to share including a webinar to watch, and one to add to your calendar, a story on SBGrid member John Buolamwini, a software release with 10 updates and 2 new applications, 2 new members to welcome, and 3 member publication highlights.
Thanks to Andrew Orry for his presentation on ICM-Browser-Pro in May. We've uploaded his webinar to our YouTube channel in case you missed it. Next on the agenda is an update from Trent Balius, of the Shoichet lab at UCSF, on DOCK in its two flavors. Details here.
For our member tale this month we turned to Rosalind Franklin University and the laboratory of John Buolamwini. Dr. Buolamwini describes his efforts to protect mitochondria from nucleoside analog drugs that have promise for treating HIV, hepatitis B, and pancreatic cancer.
Our May software release includes updates to autoPROC, BUSTER, CCP4, CYANA, Geneious, ilastik, ImageMagick, MODELLER, relax, and SAMtools. We've also added two new titles: CP2K and the open source version of PyMOL.
Two new members joined in the month of May: Marco Marcia from EMBL Grenoble and Gordon Joyce from the US Military HIV Research Program. Welcome to our newest 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 5 new citations in the month of May. Thanks to all who remembered us: Carlo Petosa at France's Institut de Biologie Structurale in Molecular Cell [Abstract]; Jason McLellan from Dartmouth in Science Translational Medicine [Abstract]; Mishtu Dey at the University of Iowa in Biochemistry[Abstract]; Virginia Commonwealth University's Montserrat Samso in Science Signaling [Abstract]; and Rockefeller's Seth Darst in Science [Abstract].
Over 80 publications from SBGrid member laboratories appeared in our latest monthly search. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- John Markley from the University of Wisconsin co-authored a review that appears in the Archives of Biochemistry and Biophysics and looks at the history and future of Biomolecular NMR [Abstract].
- As a co-author on an opinion article that appeared in Trends in Immunology, Wayne Marasco of Dana-Farber Cancer Institute proposes a deeper exploration of Ig polymorphism and antibody repertoires and a strategy to identify genotype repertoire–disease connections. [Abstract]
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a paper from Christopher Garcia's laboratory at Stanford University School of Medicine. In this Nature article Garcia reports on the success of surrogate Wnt agonists and their potential for helping future studies of Wnt signaling [More on Tumblr].
autoPROC version 20170508 is the new default. This version includes a new Table-1 like summary for each output MTZ file, several improvements to MRFANA, and added support for ALS 4.2.2 detector RDI1, along with many other improvements and fixes.
BUSTER is now at version 20170508, which includes better handling of single-atom residues when describing the structure via the TNT sequence file and several other improvements and fixes.
CP2K is new to SBGrid at version 4.1. CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
CCP4 version 7.0.038 was pushed out.
CYANA beta version 3.97 is now available via version override.
Geneious was updated to version 10.1.3. Since our last update you'll notice a new options to use DESeq2 for pairwise analysis with replicate samples for RNA seq expression analysis, to annotate nucleotide sequences from a protein database by comparing translations of the nucleotide sequence in all six frames with the protein database sequences, and to save primers used in Gibson assembly. Major changes were made for finding CRISPR sites, including improvements to the off-target scoring algorithm for CRISPR sites.
ilastik was updated to version 1.2.1
ImageMagick version 7.0.5-4 is now available.
MODELLER version 9.18 is primarily a bug fix release and adds support for Python 3.6
PyMOL Open Source version 22.214.171.124 is new to SBGrid. Users can try out this open source version of PyMOL alongside the incentive version. It was recently updated to include the Protein-Protein interface presets from the incentive version as well a fast MMTF load support.
relax version 4.0.3 is the new default. New features include per-atom RMSD calculation by the structure.rmsd user function, much faster superimposition of structures, more relax deployment scripts for Google Cloud for different GNU/Linux distributions, new OpenMPI testing scripts, and an improved relax information printout.
SAMtools is at version 1.4.1. This is primarily a bugfix release.
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.