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Dear Consortium Members and Affiliates,
For our January update, read on for details on our upcoming webinar, a profile on SBGrid member Yvain Nicolet at IBS Grenoble, a software push with 8 updates and 2 new titles, 5 new members to welcome, and 3 member publication highlights.
We hope you can join our February 14th webinar at a special time - 10am EST - with Martin Steinegger joining from Seoul, South Korea to tell us about Fast and accurate protein structure search with Foldseek. Also be sure to check the SBGrid YouTube channel, where we recently posted the December and January webinars on Proteus and NMR TITAN. Thanks to Thomas Simonson and Chris Waudby for presenting.
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This month our SBGrid tale features Yvain Nicolet from the Institut de Biologie Structurale (IBS) in Grenoble, France where his lab is on the hunt for free radicals to better understand metalloproteins. The Nicolet lab uses a series of anaerobic chambers or gloveboxes for protein expression and purification, triggering reactions and trapping intermediates using crystallography, and recently developed cryoEM techniques. [Read the full story]
This month's software push includes updates to AmberTools, autoPROC, BUSTER, CCP-EM, CcpNmr, GPHL Suite, RNA Framework, and VMD, plus two new titles: Careless and NMR TITAN. See Software Changes below for complete details.
January was the month for new institutions. All five of our new members were from institutions new to SBGrid: Jonathan Clinger from Baylor University, Mark Currie of University of Toronto, Mississauga, Oriana Fisher of Lehigh University, Dorit Hanein of University of California, Santa Barbara, and Karl-Peter Hopfner of Ludwig-Maximilians-Universität München. Welcome to our newest members!
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Member Publications Highlights |
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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:
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: |
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SBGrid citations: SBGrid's eLife paper received 8 new citations in the month since our last report, from these SBGrid-member laboratories:
Jean-Philippe Julien of University of Toronto in Clinical Cancer Research: Therapeutic Targeting of LIF Overcomes Macrophage-mediated Immunosuppression of the Local Tumor Microenvironment; Alan Brown of Harvard Medical School in Cell: Mechanism of IFT-A polymerization into trains for ciliary transport; James Letts of University of California, Davis in Nature Plants: Plant-specific features of respiratory supercomplex I + III2 from Vigna radiata; a new paper in Nature with contributions from several SBGrid members - Hao Wu from Boston Children's Hospital and Haribabu Arthanari and Eric Fischer from Dana-Farber Cancer Institute: Structural basis of regulated m7G tRNA modification by METTL1–WDR4; Andrés Palencia University Grenoble Alpes in Journal of the American Chemical Society: Adenosine-Dependent Activation Mechanism of Prodrugs Targeting an Aminoacyl-tRNA Synthetase; Yang Gao of Rice University in Journal of Biological Chemistry: Primer terminal ribonucleotide alters the active site dynamics of DNA Polymerase η and reduce DNA synthesis fidelity; and Alejandro Buschiazzo from Institut Pasteur de Montevideo in Science Signaling: An allosteric switch ensures efficient unidirectional information transmission by the histidine kinase DesK from Bacillus subtilis
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Software Changes |
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AmberTools 22 includes new and updated forcefields with lipid updates (Lipid21), a polarizable water model (OPC3-pol), and new parameters for some fluorinated amino acids, cpptraj changes with improvements to GIST improvements, a new cluster analysis, and a "prepareforleap" script with support for carbohydrates. Also new is Quick, a package for Hartree-Fock and DFT electronic structure calculations, with GPU support, an update to 3D-RISM code to support periodic boundaries and scaling for open boundaries, PyRESP, a program for RESP fitting for both additive and polariable force fields, and new constant pressure protocols for the Amber pGM polarizable force field.
autoPROC 20221121 includes initial support for different spacegroup settings, a new method of detecting significant ice-ring contamination, an option to support dynamic overload handling when using the xds-zcbf plugin, and updates to support for CCP4, CdTe Eiger detectors, HDF5 datasets.
BUSTER 20221121 includes an extension of the aB_deposition_combine tool to allow for data refinements using REFMAC or phenix.refine and improvements to aB_autorefine. Grade2 updates include a new _chem_comp.group setting for use with CIF restraint dictionaries in Coot, --lookup ID to look up a molecule in corporate or public databases for restraints generation, better control when defining the systematic ligand name, and a new option for atom naming for "non-standard" amino-acids. Careless 0.2.6 is new to the collection. Careless represents a modern, deep-learning-based approach to simultaneous merging and scaling of crystallographic data, or as the authors note, for "merging crystallography data without much physics." Be sure to mark you calendar for our May 9th webinar when developer Kevin Dalton of the Hekstra laboratory at Harvard University will introduce us to this new tool.
CCP-EM nightly release 20221108 is available via version override.
CcpNmr 3.1.0 includes lots of new features and improvements, including handling of pseudo-3D spectra, new collections and data tables to organize data, interactive shifting of 1D spectra, and the introduction of AnalysisStructure, a set of tools to assist with the structure calculation stage of biomolecular NMR projects.
RNA Framework was updated to 8596c2e.
VMD 1.9.4-alpha 55 is available via version override.
GPHL Suite, which includes autoPROC, BUSTER, and SHARP for use by for-profit users, was updated to version 20221121.
NMR TITAN is new to SBGrid at version 1.6. NMR TITAN is an easy-to-use software package for two-dimensional lineshape analysis of titration experiments from Chris Waudby's group at University College London. Thanks to Chris for introducing NMR TITAN to the SBGrid community in our January webinar: https://youtu.be/QFdJ8Gl936M.
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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 Report software bugs: sbgrid.org/bugs
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