SBGrid Consortium

GitHub - alexjnoble/VirtualIce: Half-synthetic cryoEM micrograph generator that projects pdbs>mrcs onto existing buffer cryoEM micrographs Half-synthetic cryoEM micrograph generator that projects pdbs>mrcs onto existing buffer cryoEM micrographs - alexjnoble/VirtualIce

New Title Alert: VirtualIce- a feature-rich half-synthetic cryoEM micrograph generator that uses buffer cryoEM micrographs with junk and carbon masked out as real background.

Learn more here: buff.ly/k7lsoda

#SBGrid #SBGridSoftware #StructuralBiology

GitHub - fmi-basel/RosEM: Pipeline and GUI for cryoEM model refinement using Rosetta and Phenix Pipeline and GUI for cryoEM model refinement using Rosetta and Phenix - fmi-basel/RosEM

New Title Alert: RosEM- a tool that provides easy access to the rosetta cryoem refinement protocol. The pipeline automates testing of different density weights, use of reference/starting model restraints and selections.

Learn more here: buff.ly/PFch8SF

#SBGrid #SBGridSoftware #StructuralBiology

New Member Alert:
@sciencemick.bsky.social from @ubuffalo.bsky.social joined SBGrid in June. Welcome!!

GitHub - patrickbryant1/RareFold: Structure prediction and design of proteins with noncanonical amino acids Structure prediction and design of proteins with noncanonical amino acids - patrickbryant1/RareFold

New Title Alert: RareFold- a tool for the structure prediction and design of proteins that include non-canonical amino acids.

Learn more here: buff.ly/qCffghv

#SBGrid #SBGridSoftware #StructuralBiology

New Member Alert: Tianshu Xiao from Nanyang Technological University joined SBGrid in June. Welcome!!

New Member Alert: In June, Sangwon Lee from @yaleschoolofmed.bsky.social joined SBGris. Welcome!!

GitHub - dauparas/LigandMPNN Contribute to dauparas/LigandMPNN development by creating an account on GitHub.

New Title Alert: LigandMPNN- a deep learning-based tool for designing protein sequences conditioned on atomic context, including ligands, DNA, RNA, and modified amino acids.

Learn more here: buff.ly/3llSBhI

#SBGrid #SBGridSoftware #StructuralBiology

New Member Alert: Mario Halic from @stjuderesearch.bsky.social joined SBGrid in June. Welcome!!

GetContacts Interaction analysis for molecular structures and ensembles

New Title Alert: GetContacts- a tool designed to dissect and visualize molecular interactions in proteins from various sources, including experimental structures (X-ray, NMR, Cryo-EM) and MD simulations.

Learn more here: buff.ly/L5OgZJT

#SBGrid #SBGridSoftware #StructuralBiology

GitHub - shahpnmlab/tomcat: Tomography Catalogue Tool Tomography Catalogue Tool. Contribute to shahpnmlab/tomcat development by creating an account on GitHub.

New Title Alert: Tomcat- a web-based tool designed for cataloging and managing tomography data providing an easy way to view, annotate, and organize tomograms.

Learn more here: buff.ly/75XbvPv

#SBGrid #SBGridSoftware #StructuralBiology

New Member Alert: Monica Pillon from @ubuffalo.bsky.social joined SBGrid in June. Welcome!!

EM Server Kiharalab EM Server

New Title Alert: DiffModeler- a computational tool using a diffusion model to automatically build full protein complex structure from cryo-EM maps at 0-20A resolution.

Learn more here: buff.ly/usmTRCV

#SBGrid #SBGridSoftware #StructualBiology

New Member Alert: Huanhuan Chen from University of Chicago joined SBGrid in June. Welcome!!

SBGrid's eLife paper received a citation in June from Dhirendra Simanshu & Anna Maciag from Frederick National Laboratory for Cancer Research in Science: BBO-10203 inhibits tumor growth without inducing hyperglycemia by blocking RAS-PI3Kα interaction.

Read more here: buff.ly/zOnXXwA

#SBGrid

New Title Alert: CryoTransformer- a powerful and accurate particle-picking framework using Residual Network (ResNet) and Transformer.

Learn more here: buff.ly/28aft69

#SBGrid #SBGridSoftware #StructuralBiology

Substrate recognition and allosteric regulation of synaptic vesicle glutamate transporter VGLUT2 - Nature Structural & Molecular Biology Guided by a structure of VGLUT2 with substrate, Li et al. identify the mechanisms for selective substrate recognition, a role for lipid modification in limiting axonal dispersion and for the…

SBGrid's eLife paper received a citation in June from Robert Stroud from University of California, San Francisco in @natsmb.nature.com: Substrate recognition and allosteric regulation of synaptic vesicle glutamate transporter VGLUT2.

Read more here: buff.ly/rCjNlyX

#SBGrid #StructuralBiology

SBGrid Consortium - Software Updates The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…

June's software push includes updates to BioEmu, BLAST+, Boltz-1, ChimeraX, ColabFold, Cryo_fit, cryosparc-tools, Durin, Dynamo, GROMACS, LocScale, Modeller, NAMD, PowerFit, PyEM, Pytom-match-pick, QFit, SAMtools, Scipion, Topaz, & Vesicle-Picker.

More information here: buff.ly/2BmKW9G

#SBGrid

SBGrid's eLife paper received a citation in June from Jeffrey Holt from @bostonchildrens.bsky.social along w/ Tianmin Fu of The Ohio State University, Marcos Sotomayor from University of Chicago, & Shaun Rawson from @harvardmed.bsky.social

Read more here: buff.ly/9dyEZEw

#SBGrid #StructuralBio

ccpem / ccpem-pipeliner · GitLab Python pipeliner for CCP-EM and RELION

New Title Alert: CCPEM-pipeliner- an integrated suite of software tools for processing single particle cryoEM data, from preprocessing raw image data through building and fitting atomic models.

Learn more here: buff.ly/eXK1ka2

#SBGrid #SBGridsoftware #StructuralBiology

SBGrid's eLife paper received a citation in June from @fraserlab.com of @ucsanfrancisco.bsky.social in Science Advances: Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.

Read more here: buff.ly/yzSbcp0

#SBGrid

Bacteria hunting and gathering iron. SBGrid member Andrew Gulick investigate enzymes responsible for non-ribosomal synthesis of iron transport molecules, siderophores.

@caltech.edu doctoral student Vida Robertson highlighted a new @pubs.acs.org article from SBGrid member @amgulick-lab.bsky.social at @ubuffalo.bsky.social.
Read more here: buff.ly/tkQDhx8

#SBGrid #StructuralBiology #Enzyme

In case you missed our last webinar of the season, it is now available! Genki Terashi from Purdue University presented DiffModeler and CryoREAD.

buff.ly/u2gDKMm

#SBGridWebinars #ScienceMatters

Data Collection and Processing Bootcamp | NECAT RAPD2

Community Announcements: NE-CAT is offering a 2-day Data Collection and Processing Bootcamp @ the Advanced Photon Source in Lemont, Illinois on July 24-25, 2025.

Full details: buff.ly/wxFR9v1
Spots are still available for the Bootcamp; fill out this Google form to register: buff.ly/MXaISB9

#NE-CAT

New Member Alert: In May, Evan O'Brien from Johns Hopkins University School of Medicine joined SBGrid. Welcome!!

New Title Alert: xtb- (extended tight binding) implements the semiempirical quantum mechanical methods GFNn-xTB, their descendants, and corresponding composite schemes.

Learn more here: buff.ly/aYIMQE1

#SBGrid #Software #StructuralBiology

GitHub - ELELAB/RosettaDDGPrediction Contribute to ELELAB/RosettaDDGPrediction development by creating an account on GitHub.

New Title Alert: RosettaDDGPrediction- a Python package to run Rosetta-based protocols for the prediction of the ΔΔG of stability upon mutation of a monomeric protein or the ΔΔG of binding upon mutation of a protein complex and analyze the results.

Learn more here: buff.ly/VGgnaLB

#SBGridsoftware

New Member Alert: In May, Ali Hamiche from Institute of Genetics, Molecular and Cellular Biology joined SBGrid. Welcome !!

PsiCode PsiCode

New Title Alert: Psi4- is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of molecular properties.

Learn more here: psicode.org

#SBGridSoftware #StructuralBiology

New Member Alert: Abdullah Al Mamun from Meharry Medical College joined SBGrid in May. Welcome!

GitHub - lovakap/OutlierRemoval: Partcile sorting Partcile sorting. Contribute to lovakap/OutlierRemoval development by creating an account on GitHub.

New Title Alert: OutlierRemoval- is an implementation of outlier removal in cryo-electron microscopy (cryo-EM) datasets using radial profiles. The method focuses on removing outliers to enhance the quality of the 2D class averages and downstream analysis.

Learn more here: buff.ly/Ws62zQr

#SBGrid