#SBGrid Software Webinars will resume in October - Tuesdays at 12pm EDT/EST-Registration information coming soon.
Tues, October 10, 2023: ScipionTomo
Pablo Conesa, Team Leader, Spanish Council for Scientific Research

Tues, November 14, 2023: DiffDock
Gabriele Corso, Hannes Stärk, & Bowen Jing, Ph.D. students, MIT Computer Science & Artificial Intelligence Laboratory (CSAIL)

Tues, December 12, 2023: DeepFoldRNA
Robin Pearce, Ph.D. student, Yang Zhang's lab, University of Michigan Medical School

Meharry Medical College student KeAndreya Morrison highlighted a publication with contributions from Andreas Plückthun's group that appeared in Gene Therapy and describes a novel all-in-one shock and kill method for HIV-1 therapy that shows a promising way to eliminate infected cells in a specific T-cell and HIV-1 manner.

https://www.tumblr.com/sbgridconsortium/727088151128096768/all-in-one-shock-and-kill-therapies-could-be-the?source=share

#sbgrid
#science
#biomedicalresearch
#crispr
#therapeutic

SBGrid's eLife paper was cited by SBGrid member M. Gordon Joyce U.S. Military HIV Research Program in Journal of Virology.

Read more at: Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity

https://journals.asm.org/doi/full/10.1128/jvi.01596-22?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=457&lea=24537&ctr=0&par=1&trk=a0N3s00000PtIByEAN

<ALT= Crystal structure and epitope analysis of the SARS-CoV-2 RBD with WRAIR-2063 Fab>

#Science #virology #antibodies #SBGrid

SBGrid's eLife paper received a new citation in the month of July from #SBGrid member James A. Letts from University of California, Davis, Davis in Nature Plants.

Read more at: Plant-specific features of respiratory supercomplex I + III2 from Vigna radiata

Authors: M. Maldonado, Z. Fan, K. M. Abe, & J. A. Letts

https://escholarship.org/content/qt4s17c340/qt4s17c340_noSplash_701ed92b41be6801ffd6db0ba3e3c23d.pdf?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=457&lea=24537&ctr=0&par=1&trk=a0N3s00000PtIByEAN

SBGrid's eLife paper received a new citation in the month of July from SBGrid member Marc Kvansakul at La Trobe University in Nature Communications Biology: Membrane recruitment of the polarity protein Scribble by the cell adhesion receptor TMIGD1

Read more at: https://www.nature.com/articles/s42003-023-05088-3?utm_

#SBGrid #science #protein #membranes

SBGrid's eLife paper received a new citation in the month of July from #SBGrid member Dirk Slotboom from University of Groningen in Nature Communications: Expulsion mechanism of the substrate-translocating subunit in ECF transporters.

https://www.nature.com/articles/s41467-023-40266-1?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=457&lea=24537&ctr=0&par=1&trk=a0N3s00000PtIByEAN

<ALT= Conformational states of ECF transporters>

New Title Alert: Fidder is a Python package for detecting and erasing gold fiducials in cryo-EM images.

https://teamtomo.org/fidder/

#science #cryo-EM #research #SBGrid

New Title Alert: MemBrain-Seg is new to the #SBGrid software collection. This is a Python project developed by teamtomo for membrane segmentation in 3D for cryo-electron tomography (cryo-ET). This tool aims to provide researchers with an efficient and reliable method for segmenting membranes in 3D microscopic images.

https://github.com/teamtomo/membrain-seg

#electronmicroscopy #science #cryo-ET #membranes

Fisk University graduate student Vida Robertson's July highlight features a publication from SBGrid Consortium member Stephen Burley of the RCSB Protein Data Bank, Rutgers University, which appears in JCI Insight and describes the authors crafting of a computational pipeline able to predict how COVID-19 mutations affect the infectivity of variants.
https://www.tumblr.com/sbgridconsortium/724367393390018560/using-the-pdb-to-predict-how-covid-mutations?source=share

<ALT= Receptor binding domain of COVID-19 (blue) binding to ACE2 (green). PDB:7T9L>

#SBGrid #Science #COVID-19 #mutations

New Title Alert: RFdiffusion is new to the #SBGrid software collection. This is an open source method for structure generation, with or without conditional information (a motif, target etc). It's a powerful new way to design proteins by combining structure prediction networks and generative diffusion models.

https://www.bakerlab.org/2023/07/11/diffusion-model-for-protein-design/

Read more at
De novo design of protein structure and function with RFdiffusion

https://www.nature.com/articles/s41586-023-06415-8

#structuralbiology #Science #research #proteinstructure

Meharry Medical College graduate student KeAndreya Morrison highlighted a Cell Reports publication with contributions from SBGrid member Peter Kwong of the National Institute of Allergy and Infectious Diseases (NIAID) in which the authors describe improved HIV neutralizing antibodies using OSPREY, an open-source protein design software.

https://www.tumblr.com/sbgridconsortium/724367027985416192/a-new-method-for-hiv-antibody-design

#science #SBGrid #antibodies #cryoem #research

<ALT= Cyro-EM structure of PG9RSH Y(100k)D variant>

SBGrid's eLife paper received a new citation in the month of June from #SBGrid member 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.
https://journals.asm.org/doi/full/10.1128/mbio.00631-23?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=456&lea=24537&ctr=0&par=1&trk=a0N3s00000PU74ZEAT

SBGrid's eLife paper received a new citation in the month of June from #SBGrid member Dhirendra K. Simanshu of the Frederick National Laboratory for Cancer Research in Nature Communications Biology; Reduced dynamic complexity allows structure elucidation of an excited state of KRASG13D.
https://www.nature.com/articles/s42003-023-04960-6?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=456&lea=24537&ctr=0&par=1&trk=a0N3s00000PU74ZEAT

Technical Notes: Our June software push includes updates to BioXTAS RAW, careless, DIALS, DiffDock, IMOD, OpenMM, RNA Structure, ShapeMapper2, Topaz, Xplor-NIH.

https://sbgrid.org/software/recent/archive/

#SBGrid #Software #Crystallography #cryoem #molecules

Technical Notes: New titles in June include cs2star, Deep Finder, DeltaVina, EMReady, GWOVina, imod2relion, MMseqs2, and TomoDRGN.
https://sbgrid.org/software/

#SBGrid #Science #Software #NMR

Meharry Medical College graduate student KeAndreya Morrison highlighted a publication in PLOS One from Vanderbilt University SBGrid members Tina M. Iverson & Terunaga Nakagawa, w/Prashant Singh, who describe co-expression of multiple MS-ring domains with the C-ring of the flagellar motor to reveal the MS-ring’s ability to adopt more than one stoichiometry.
https://sbgridconsortium.tumblr.com/post/721404577059045376/new-structure-of-flagellar-motor-component?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=456&lea=24537&ctr=0&par=1&trk=a0N3s00000PU74ZEAT
#science #SBGrid #cryoem
<ALT= Top view (left) and side view (right) of the post assembly structure of the MS-ring>

Fisk University graduate student Vida Robertson highlighted a publication from the laboratory of Ming Zhou Baylor College of Medicine. The authors investigated the loss of enzymatic activity in Stearoyl-CoA desaturase-1 (SCD1) over time & used UV-vis spectroscopy, EPR, & inductively coupled plasma mass spectrometry to implicate a loss of iron at the active site as one cause.
https://sbgridconsortium.tumblr.com/post/721470101341224960/understanding-how-iron-affects-stearoyl-coa?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=456&lea=24537&ctr=0&par=1&trk=a0N3s00000PU74ZEAT

#SBGrid #Science #biomedical
<Alt= Published structure of SCD-1 diiron active site. PDB: 6WF2>

SBGrid's eLife paper received a new citation in the month of June from #SBGrid member Ryan Hibbs of University of Texas Southwestern Medical Center in Nature Communications: Structural interplay of anesthetics and paralytics on muscle nicotinic receptors.
https://www.nature.com/articles/s41467-023-38827-5?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=456&lea=24537&ctr=0&par=1&trk=a0N3s00000PU74ZEAT

In our SBGrid Tale for the month of June, we're featuring André Hoelz from Caltech, 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

https://sbgrid.org/members/tale/the-monstrous-maw?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=456&lea=24537&ctr=0&par=1&trk=a0N3s00000PU74ZEAT

#technology #science #SBGrid

Available on our Youtube channel is 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.
https://www.youtube.com/watch?v=demzYpT2IaQ&feature=youtu.be

#software #NMR #Biomolecules #science #SBGrid