Dear Consortium Members and Affiliates,
Greetings from the SBGrid team, where the heat wave finally made its way to New England. Our July update includes a reminder about annual renewal invoices, a profile on SBGrid member Evripidis Gavathiotis, a software push with 13 updates and 4 new tools, 4 new members to welcome, and 3 member publication highlights.
Renewal invoices went out in July to all SBGrid members. Many thanks to all who have already initiated payment! Please be sure to check your spam folders if you haven't found a renewal an email from us. We are encouraging electronic payments (credit card, wire, ACH) when possible to avoid mail processing delays. Let us know if any changes are needed and complete payment or notify us with a purchase order number or wire transfer details by Aug 31.
For our July SBGrid Tale we chatted with Evris Gavathiotis in his laboratory at Albert Einstein College of Medicine, whose made a career out of life and death. Gavathiotis had big ideas from an early age, when his mother's chronic illness and his love of chemistry propelled him toward science. He has since spent his time orchestrating when cells live or die to treat diseases including cancer, neurodegneration, heart attacks, Alzheimer's disease, and diabetes. [Read the full story].
We had four new members join in July: Henning Stahlberg from Ecole Polytechnique Fédérale de Lausanne, Lijun Sun from Beth Israel Deaconness Medical Center, Minu Chaudhuri from Meharry Medical College, and Shu-ou Shan of Caltech. 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 6 new citations in the month of July, from these SBGrid-member laboratories:
Ekaterin Heldwein from Tufts University School of Medicine in PLOS Pathogens: The nuclear egress complex of Epstein-Barr virus buds membranes through an oligomerization-driven mechanism; Ryan Hibbs from the University of Texas Southwestern Medical Center in Cell: Structural mechanisms of GABAA receptor autoimmune encephalitis; Anthony Kossiakoff from University of Chicago and Tom Rapoport of Harvard Medical School in Nature: A peroxisomal ubiquitin ligase complex forms a retrotranslocation channe; John Pascal at the University of Montreal in Molecular Cell: Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery; Sichen Shao of Harvard Medical School and Philip Kranzusch of Dana Farber Cancer Institute in Nature: Cryo-EM structure of an active bacterial TIR–STING filament complex; Lawrence Stern from University of Massachusetts Medical School in ACS Chemical Biology: Phenylsulfamoyl Benzoic Acid Inhibitor of ERAP2 with a Novel Mode of Inhibition
AreTomo 1.2 is now available and includes the smart grid technique recently developed in MotionCor2 1.5.0, refinement of the tilt axis, improved projection matching alignment, and an implementation of multiple GPUs.
ATSAS was updated to version 3.1.1
BioXTAS RAW 2.1.4 is compatible with ATSAS 3.1.0. Because of ATSAS changes you may notice changes to associated RAW tools: CIFSUP replaces SUPCOMB, DAMCLUST is included in DAMAVER and is no longer an option in the DAMMIF/N GUI, SASRES is not included in DAMAVER 3.1.1 output, output formats for DAMMIF/N are now .cif files, improved speed with multi-core DAMAVER, but note that users cannot restrict the number of cores used. Clustering results from DAMAVER no longer include average cluster deviation or distance between clusters.
CCP4 8.0.002 includes updates to crank 2, ccp4 cloud, ccp4mg, modelcraft, and a bug fix in mrbump.
COOT is now at release 1.005.
cryoDRGN 1.1.0 is the new default. With the jump to 1.0 users will find several new tools for analysis of the reconstructed ensembles and new functionality for calling utility scripts with cryodrgn_utils
CrystFEL 0.10.1 is largely a bug fix release. Full details in these release notes.
crYOLO version 1.8.4 is the new default. It fixes a dependency problem of protobuf and updates filament tracing to use a chunksize of 1 to utilize the processor more efficiently.
Fiji was updated to include a couple of additional plug-ins:
- LabKit: a user-friendly Fiji plug-in for the segmentation of microscopy image data.
- MicrobeJ: an ImageJ plug-in to analyze bacterial cells.
Geneious Prime 2022.2 includes improvements for cloning and data import, including:
in-fusion cloning, parts cloning support for proteins, primer extension detection, and data sync using the Command Line Interface
GROMACS 2022 is out, now at release 2022.2. This update includes many performance improvements with or without GPUs in addition to SIMD-accelerated free-energy kernels that speed free-energy calculations, finer control of the alchemical transformation pathways, arbitrary mathematical transformations of one of more other pull coordinates, a new interface for multi-scale Quantum Mechanics / Molecular Mechanics (QM/MM) simulations with the CP2K quantum chemistry package, grompp performance improvements, Cool quotes music playlist, and many improvements to GPU support.
IMOD release 4.11.18 is out.
IsoNet version 0.2
Modeller 10.3 is a minor update that fixes the mod10.3 compatibility script on
Proteus 3.0 is new to SBGrid. Proteus is a general purpose program for protein design, to redesign entire proteins or functional sites such as ligand-binding pockets. It uses a physics-based energy function and a stochastic method to search sequence and conformation space and allows users to directly select mutations that increase ligand binding free energy or ligand specificity. It can perform constant-pH Monte Carlo, which yields acid/base constants or pKa’s.
subTOM 1.1.6 is also new to SBGrid. SubTOM is a collection of s ubtomogram averaging scripts with TOM toolbox.
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.
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More information about the SBGrid Consortium is available at https://sbgrid.org
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