SBGrid Newsletter: November 2024 |
Dear Consortium Members and Affiliates,
We're delivering our November newsletter a few days early in anticipation of the Thanksgiving holiday. Read on for details on holiday closures, a profile on SBGrid member Jens Meiler, our upcoming webinar on AreTomo3, a software push with six updates and five new titles, severn new members to welcome, and two publication highlights.
SBGrid offices will close on Thursday November 28 for the Thanksgiving holiday, and reopen on Monday, December 2. Happy Holidays to all who celebrate and best wishes for a some recuperative downtime with friends and family.
For our November member tale we caught up with SBGrid member Jens Meiler, who splits his time between laboratories at Vanderbilt and Leipzig Universities and offers some perspective around the ongoing AI frenzy. Meiler remembers designing his first predictive neural network as an undergraduate and making use of some of that code in his early contribution to Rosetta. He looks to the future when tools like AlphaFold are combined with biophysical technologies toward a more personalized structural biology. [Read the full story]
Join us on December 10th for our software webinar series, when we'll hear from Ariana Peck, Data Scientist at CZ Imaging Institute, on AreTomo3: Real-time Processing Pipeline for Generating 1,000 Accurate and Contrast-Enhanced Tomograms [Register here].
In case you missed our October webinar on AquaRef, with Pavel Afonine of Berkeley Lab, the video is now available on the SBGrid YouTube channel.
To receive email reminders about upcoming webinars, please be sure to register for the series! Registration here: https://sbgrid.org/webinars/#register |
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Dec 10: AreTomo3: Real-time Processing Pipeline for Generating 1,000 Accurate and Contrast-Enhanced Tomograms - Ariana Peck
Jan 14: MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography - Lorenz Lamm
Feb 11: Phenix/OPLS and GlideEM: Enabling cryoEM structures for drug discovery with the Schrodinger Suite - João Rodrigues
Mar 11: Structure modeling and Validation using AI-based methods: DeepMainmast and DAQ - Genki Terashi
April 8: Warp - Dimitry Tegunov
May 13: DRGN-AI - Ellen Zhong
Webinar registration and details |
SBGrid webinars are hosted with partial support from the NIH R25 Continuing Education for Structural Biology Mentors #GM151273, in collaboration with Co-PI Jamaine Davis of Meharry Medical College. |
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This month's software push includes updates to AreTomo, CcpNmr, cryoDRGN, ModelAngelo, POKY, and Starparser, along with five new titles: Ais, Boltz-1, DeepFRI, GisSPA, and MiloPYP. See Software Changes below for complete details.
Seven new members joined during November: Alireza Ghanbarpour of Washington University in St. Louis, Montserrat Samso of Virginia Commonwealth University, Sean Whelan of Washington University in St. Louis, Duncan Sousa at the Beckman CryoEM Center at Johns Hopkins University School of Medicine, and Clément Charenton and Florian Faessler from Institute of Genetics and Molecular and Cellular Biology. Welcome to our newest members! |
Member Publication Highlights |
From our graduate student desk |
Over 100 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:
- Fisk University student Vida Storm Robertson highlighted a publication from SBGrid member Dirk Slotboom from University of Groningen and his colleague Anna Hirsch of Helmholtz Centre for Infection Research that appeared in Protein Science and describes the authors' investigation of a new druggable target for treating pneumonia infections. [Read more]
- Meharry Medical College student KeAndreya Morrison's highlight features a publication from the laboratory of Douglas Kojetin of Vanderbilt University and colleagues that appeared in eLife and describes how PPARγ, a key protein involved in metabolism and blood sugar regulation, can bind both a covalent inhibitor and a synthetic drug simultaneously, revealing new ways to enhance treatments for diabetes and other metabolic disorders. [Read more]
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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: |
Structural biology applications used in this project were compiled and configured by SBGrid [1]. [1] A. Morin, B. Eisenbraun, J. Key, P. C. Sanschagrin, M. A. Timony, M. Ottaviano, and P. Sliz, “Collaboration gets the most out of software.,” Elife, vol. 2, p. e01456, Sep. 2013.
Link to article: https://elifesciences.org/articles/01456. |
Ais 20241112 is new to SBGrid. Ais provides annotation and segmentation of cryo-ET data using convolutional neural networks.
AreTomo3 version 2.0.1 introduces a number of changes and bug fixes. Please see the Readme.txt file for versions 2.0.0 and 2.0.1.
Boltz-1 0.1.0 is also new. Boltz-1 is an open-source model that predicts the 3D structure of proteins, RNA, DNA, and small molecules. It handles modified residues, covalent ligands, and glycans, and conditioning support for pocket residues. CcpNmr 3.2.2.1 includes news features for 1D metabolomics, including unknown substance simulations and simulated 1H spectra, alongside various bug fixes. cryoDRGN 3.4.2 introduces significant performance improvements to several existing features: uses mixed precision training for abinit_homo and abinit_het, 100x improvement to parse_pose_star with vectorized rotation matrix computation, and a 10x increase to analyze_landscape_full. DeepFRI 1.0.0 is another new title. DeepFRI is a software tool that employs deep learning to predict protein functions and identify key functional regions.
GisSPA 1.1.2 is another new one. GisSPA is a GPU-accelerated program that uses single cryo-electron microscopy images without tilt-series to translationally and rotationally localize the target protein complex in cellular lamellae, as prepared with a focused ion beam, and reconstructs the protein complex at near-atomic resolution.
MiLoPYP 0.5.0 is the last of the new titles. MiLoPYP is a two-step, dataset-specific, contrastive learning-based framework that enables fast molecular pattern mining followed by accurate protein localization. ModelAngelo 1.0.13 fixes an issue with more chain breaks caused by extra sharpening of predicted amino acid logits in flood_fill.py. POKY 20240829 includes multiple bugfixes and updates to the nmrglue module to handle data acquired under legacy versions of TopSpin.
Starparser versions 1.57 and 1.58 were pushed out and include updates to particleplay, plots, and decsiontree() functions following the developers' git repo. |
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.
More information about the SBGrid Consortium is available at https://sbgrid.org
Report software bugs: sbgrid.org/bugs |
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