Dear Consortium Members and Affiliates,
It's time for a monthly recap from the SBGrid team. In June we wrapped up our webinar series and posted the latest video to YouTube, met up with SBGrid member André Hoelz to learn more about the work happening in his Caltech laboratory, pushed out 10 software updates and 8 new titles, welcomed 8 new members, and published highlights on 2 member publications.
Our June software webinar was the last season, with a presentation from Woonghee Lee on one of the newer software titles in the collection: POKY - a software suite for multi-dimensional NMR and 3D structure calculation of biomolecules. We also spent the last couple of months making accessibility improvements and adding closed captioning for all of the videos for this webinar season. Learn more about POKY and many other software titles in the SBGrid collection on the SBGrid YouTube channel.
In our SBGrid Tale for the month of June, we're featuring André Hoelz from
California Institute of Technology, whose decade-long work on the nuclear pore complex contributed to the composite structure of the complex that made the cover of a special issue of Science in 2022. Hoelz is now cooking up new avenues of discovery for his lab along with his specialty dish: tarte flambée. [Read the full story].
Our June software push includes updates to BioXTAS RAW, careless, DIALS, DiffDock, IMOD, OpenMM, RNA Structure, ShapeMapper2, Topaz, Xplor-NIH and a flurry of new titles: cs2star, Deep Finder, DeltaVina, EMReady, GWOVina, imod2relion, MMseqs2, and TomoDRGN. See Software Changes below for complete details.
Eight new members joined in the past month: Marc Delarue, Pablo Guardado-Calvo, Ahmed Haouz, and Felix Rey from Institut Pasteur in France, Fikri Avci and Stefan Sarafianos from Emory University School of Medicine, Arvin Dar from Memorial Sloan Kettering Cancer Center, and Chad Rienstra from University of Wisconsin-Madison. Welcome to our newest members!
Member Publications Highlights
FROM OUR GRADUATE STUDENT DESK
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.
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's eLife paper received 5 new citations in the month of June, from these SBGrid-member laboratories:
Alan Brown of Harvard Medical School in Nature Axonemal structures reveal mechanoregulatory and disease mechanisms; Christopher Garcia at Stanford University in Cell Reports: A structural blueprint for interleukin-21 signal modulation; Ryan Hibbs of University of Texas Southwestern Medical Center in Nature Communications: Structural interplay of anesthetics and paralytics on muscle nicotinic receptors; Dhirendra Simanshu at Frederick National Laboratory for Cancer Research in Nature Communications Biology: Reduced dynamic complexity allows structure elucidation of an excited state of KRASG13D; and Elizabeth Wright of University of Wisconsin-Madison in Genetics and Molecular Biology: The role of CenKR in the coordination of Rhodobacter sphaeroides cell elongation and division
BioXTAS RAW 2.2.0 includes integration of CRYSOL into the GUI and API to allow theoretical profiles by simply plotting a .pdb or .cif file, or by opening the CRYSOL analysis window and adjusting the settings and fit the model to experimental data. Also new is a profile comparison window that provides residual and ratio plot, faster calculation of SVD and forward and backward EFA plots, and an improved PDF report with text wrapping in columns so that tables can’t extend off the edge of the page and vector graphics plots.
careless 0.2.9 now outputs merged intensities in addition to structure factors.
cs2star 0.5.4 is new to the SBGrid collection. cs2star is a simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.
Deep Finder 20230510 is another new SBGrid title. Deep Finder is an original deep learning approach to localize macromolecules in cryo electron tomography images. The method is based on image segmentation using a 3D convolutional neural network.
DeltaVina 20230614 was also added this month. DeltaVina is a scoring function for rescoring protein-ligand binding affinity.
DIALS 3.14.2 has a dxtbx compatibility fix for the DECTRIS Eiger FileWriter.
DiffDock was updated to latest - 3d45728.
EMReady 20230606 makes 4 in the new software list. EMReady improves the quality and interpretability of cryo-EM maps by local and non-local deep learning.
GWOVina 1.0 (you guessed it) is also new. GWOVina is based on the implementation of AutoDock Vina and employs grey wolf optimization (GWO) algorithm to speed up the search for optimal ligand poses.
IMOD updates to 4.11.24 (default) and 4.12.47 (available via version override) are available.
imod2relion was added to SBGrid at version. 1.1.0. imod2relion is a tool that reads IMOD points, obtains particle information and generates .star file for RELION.
MMseqs2 version 14-7e284 is new software number 7. MMseqs2 is an ultra fast and sensitive sequence search and clustering suite.
OpenMM 8.0.0 is out with better support for machine learning potentials for use with OpenMM-Torch and OpenMM-ML plugins many optimizations on the CPU platform, new support for per-particle computed values in CustomNonbondedForce, a new boxShape option for building non-rectangular boxes in Modeller.addSolvent(), improved support for low end GPUs that don't support 64-bit atomic operations on OpenCL platform, and a change to report the system temperature when simulating a system with Drude particles.
RNA Structure 6.4 is the new default. This version adds a new --stemloop option to calculate hairpin stemloop probabilities to ProbScan, --DMS mode to Rsample, and --alphabet option to use alternative folding alphabets to AllSub, bifold, bipartition, and DuplexFold. Also new is a revised scorer that ignores nucleotide identities and a fix to a problem with m6A thermodynamic parameter files.
ShapeMapper2 version 2.2 adds a DMS mode option, fixes a bug in MutationParser so that paired (unmerged) reads are now merged, and provides a temporary fix to STAR mode so that it automatically runs in serial, avoiding the hang that happens in parallel.
Topaz 0.2.5a had a correction pushed. Version 0.2.5_cu11.2 is the latest default version for the release built on Topaz 0.2.5 and CUDA 11.2. The previous default Topaz version in SBGrid, 0.2.5_cu11, was incorrectly built on Topaz 0.2.4.
TomoDRGN 0.2.2 is the last of the new software titles in June. TomoDRGN extends the cryoDRGN framework to cryo-ET by learning heterogeneity from datasets in which each particle is sampled by multiple projection images at different stage tilt angles.
Xplor-NIH 3.7 includes a new PASD facility for automatic assignment for enhancement and optimization of the initMatch stage and better handling of inter-molecular restraints.
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