Dear Consortium Members and Affiliates,
The academic season has begun and with it the pace ratchets up a few notches. News from the SBGrid front includes a new round of software webinars, a profile on SBGrid member Jamaine Davis at Meharry Medical College, a software push with seven updates and five new titles, twelve new members to welcome, and three member publication highlights.
For our 2022-23 Software Webinar Series, we are featuring several software titles new to SBGrid and are grateful to the developers for agreeing to introduce us to these tools. See full details and how to register for the series at sbgrid.org/webinars/. You can also watch webinars from past years on the SBGrid YouTube channel.
For our September SBGrid Tale, we connected with Jamaine Davis of Meharry Medical College in Nashville, Tennessee, where his lab uses structural biology as a tool to understand biological health disparities. Davis emphasizes the importance of using his position not only to advance science, but also to act as mentor and role model, and has more recently stepped into the role of community advocate. [Read the full story].
Our September software push includes updates to AlphaFold, bcftools, CCP4, mdanalysis, PyEM, RStudio, and Samtools, along with 5 new software titles: AlphaPulldown, DAQ, RD Kit, ProteinMPNN, RoseTTAFold. See Software Changes below for complete details.
We had 12 new members join in September: Mario Bianchet at Johns Hopkins School of Medicine, Kristina Djinovic Carugo from EMBL Grenoble, Fei Guo for the BioEM facility at University of California Davis, Kizzmekia Corbett at Harvard School of Public Health, David Friedman from Beth Israel Deaconness Medical Center, Stuart Orkin of Boston Children's Hospital, Joost Snijder of Utrecht University, from University of Cincinnati Medical School, Desiree Benefield at the Center for Advanced Structural Biology, Xiaowei Hou, Rhett Kovell, and Thomas Thompson, and some folks at BioNTech. Welcome to our newest members!
Member Publications Highlights
Over 90 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple of notable highlights below:
Deposit your experimental datasets: If you're currently preparing a manuscript, please remember that, while you're making the PDB record deposit and publication submission, you can also preserve your primary experimental datasets with deposits to the SBGrid Data Bank.
Acknowledge SBGrid: SBGrid operations are funded with member fees and grants, so we are grateful when you are able to acknowledge SBGrid in your presentations and publications.
Please use this SBGrid logo on the acknowledgements slide of your presentations.
We recommend the following boilerplate language for inclusion in publications that report results obtained with SBGrid supported software:
SBGrid citations: SBGrid's eLife paper received one new citations in the month of September in a Protein Science publication with contributions from SBGrid member Thomas Schwartz at MIT: Structure and Specificity of an Anti-Chloramphenicol Single Domain Antibody for Detection of Amphenicol Residues
AlphaFold 2.2.4 is a bug fix release.
AlphaPulldown was added to the collection at version 0.21.5. AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer.
bcftools 1.16 is out. This release includes a new plugin - bcftools +variant-distance - to annotate records with distance to the nearest variant, support for querying of multiple filters, for example -i 'FILTER="A;B"' can be used to select sites with two filters "A" and "B" set.
CCP4 was updated to release 8.0.004.
DAQ is new to SBGrid with the 20220816_7ee5f50. DAQ is a computational tool that uses deep learning to estimate the residue-wise local quality for protein models from CryoEM maps.
MDAnalysis was updated to version 2.2.0, which drops support for Python 3.7 and raises the minimum versions for a number of other packages. Refer to notes linked above for details.
ProteinMPNN 20220819 is another new title. ProteinMPNN is a deep learning-based protein sequence design method.
PyEM release 20220131 is now available.
RD Kit at release 2022.03.5 is another new tool. RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
RoseTTAFold makes the fifth new title this month. RoseTTAFold is used for accurate prediction of protein structures and interactions using a 3-track network.
RStudio 2022.02.3 is available via version override and includes support for v2 format of Quarto crossref index along with a number of fixes.
Samtools 1.16.1 is a bug fix 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.
This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium, the Structural Biology Grid computing consortium.
More information about the SBGrid Consortium is available at https://sbgrid.org
Report software bugs: sbgrid.org/bugs