#structuralbiology — Public Fediverse posts

Who we are looking for
You are finishing or have recently finished an MSc in computational biology, bioinformatics, or a related field. What matters most is that you have a good understanding of biological networks, and good computational skills.
Required
    • Strong Python and the scientific stack (NumPy, pandas)
    • Experience handling protein structure data (PDB/mmCIF, AlphaFold DB) and building reproducible data pipelines over thousands of structures
    • Working knowledge of network and graph analysis (NetworkX, igraph, clustering and community detection)
    • Familiarity with biological interaction and annotation resources (STRING, BioGRID, UniProt, disease gene sets such as OpenTargets or DisGeNET)
    • Benchmarking rigor: you understand precision/recall trade-offs, how to build fair negative sets, and how to spot circularity
    • Ability to read a published method and reproduce its analysis from paper plus code
    • Good scientific writing and communication in English

Duration: 6 months
Paid: CHF 2,200 gross monthly

#gefedihired #switzerland #epfl #bioinformatics #StructuralBiology #StructuralBiology

Who we are looking for
You are finishing or have recently finished an MSc in computational biology, bioinformatics, or a related field. What matters most is that you have a good understanding of biological networks, and good computational skills.
Required
    • Strong Python and the scientific stack (NumPy, pandas)
    • Experience handling protein structure data (PDB/mmCIF, AlphaFold DB) and building reproducible data pipelines over thousands of structures
    • Working knowledge of network and graph analysis (NetworkX, igraph, clustering and community detection)
    • Familiarity with biological interaction and annotation resources (STRING, BioGRID, UniProt, disease gene sets such as OpenTargets or DisGeNET)
    • Benchmarking rigor: you understand precision/recall trade-offs, how to build fair negative sets, and how to spot circularity
    • Ability to read a published method and reproduce its analysis from paper plus code
    • Good scientific writing and communication in English

Duration: 6 months
Paid: CHF 2,200 gross monthly

#gefedihired #switzerland #epfl #bioinformatics #StructuralBiology #StructuralBiology

What you will do
    1. Run PeSTo Screen all-against-all over a large set of human proteins to generate a predicted interaction network.
    2. Deploy and characterize the results against reference interaction databases such as STRING, to see how well the predictions line up with known biology.
    3. Recreate ATOMICA’s disease-network analysis on your PeSTo Screen network, overlay disease-associated genes, and test which approach recovers disease pathways more cleanly. Comparison to ATOMICA is the core deliverable.

Optional extension
If time allows and depending on model scope, benchmark PeSTo Screen on standardized external tasks such as the RNAGlib RNA structure-function benchmark, and other.

#gefedihired #switzerland #epfl #bioinformatics #StructuralBiology #StructuralBiology

What you will do
    1. Run PeSTo Screen all-against-all over a large set of human proteins to generate a predicted interaction network.
    2. Deploy and characterize the results against reference interaction databases such as STRING, to see how well the predictions line up with known biology.
    3. Recreate ATOMICA’s disease-network analysis on your PeSTo Screen network, overlay disease-associated genes, and test which approach recovers disease pathways more cleanly. Comparison to ATOMICA is the core deliverable.

Optional extension
If time allows and depending on model scope, benchmark PeSTo Screen on standardized external tasks such as the RNAGlib RNA structure-function benchmark, and other.

#gefedihired #switzerland #epfl #bioinformatics #StructuralBiology #StructuralBiology

Internship project: Benchmarking PeSTo Screen against ATOMICA for molecular interaction networks
About us
Lemna Bio is an EPFL spin-off building structural AI models that reason about how molecules interact, directly from 3D structure. Our published model PeSTo predicts interaction interfaces on proteins. We are now extending it into PeSTo Screen, a model that performs all-against-all interaction screening: given large sets of molecules, it scores how likely each pair is to interact, in a single fast pass rather than by brute-force docking.

The project
A recent model from the Zitnik lab at Harvard, ATOMICA, learns representations of molecular interfaces and uses them to build interaction networks and recover disease-associated pathways. ATOMICA connects proteins by how similar their interfaces look. PeSTo Screen takes a different route: it predicts whether two proteins actually interact. This project asks a clear question: does predicting interactions directly recover biology better than comparing interface similarity?
You will benchmark PeSTo Screen head to head against ATOMICA, using ATOMICA’s own published analyses as the yardstick.

#gefedihired #switzerland #epfl #bioinformatics #StructuralBiology #StructuralBiology

Internship project: Benchmarking PeSTo Screen against ATOMICA for molecular interaction networks
About us
Lemna Bio is an EPFL spin-off building structural AI models that reason about how molecules interact, directly from 3D structure. Our published model PeSTo predicts interaction interfaces on proteins. We are now extending it into PeSTo Screen, a model that performs all-against-all interaction screening: given large sets of molecules, it scores how likely each pair is to interact, in a single fast pass rather than by brute-force docking.

The project
A recent model from the Zitnik lab at Harvard, ATOMICA, learns representations of molecular interfaces and uses them to build interaction networks and recover disease-associated pathways. ATOMICA connects proteins by how similar their interfaces look. PeSTo Screen takes a different route: it predicts whether two proteins actually interact. This project asks a clear question: does predicting interactions directly recover biology better than comparing interface similarity?
You will benchmark PeSTo Screen head to head against ATOMICA, using ATOMICA’s own published analyses as the yardstick.

#gefedihired #switzerland #epfl #bioinformatics #StructuralBiology #StructuralBiology

Lemna Bio (lemna.bio), an #EPFL spin-off building structural AI models that reason about how molecules interact, directly from 3D structures, is looking for a (paid!) intern to benchmark their newly developed models. Details in the reply to this toot; DM me if interested, feel free to pass it along your network if you know someone who might be interested.

Please only candidates already based in Switzerland.

#getfedihired #switzerland #bioinformatics #StructuralBiology

Lemna Bio (lemna.bio), an #EPFL spin-off building structural AI models that reason about how molecules interact, directly from 3D structures, is looking for a (paid!) intern to benchmark their newly developed models. Details in the reply to this toot; DM me if interested, feel free to pass it along your network if you know someone who might be interested.

Please only candidates already based in Switzerland.

#getfedihired #switzerland #bioinformatics #StructuralBiology

Technical Notes: July's software push includes updates to 20 titles --- BCFtools, Blast+, Chimera, CcpNmr Analysis, Fiji, GROMACS, Icecream, IMOD, LigPlot+, MODELLER, NMRPipe, OpenEye, OpenFold3, RDKit, SAMtools, Schrödinger, Scipion, TEMPy-ReFF, tomoDRGN, and Warp.

More here: https://sbgrid.org/software/recent/archive/2026/07/

#SBGrid #Software #StructuralBiology

Researchers have uncovered how a specific protein, latent TGFβ-binding protein 1 (LTBP1), regulates and stabilizes transforming growth factor beta (TGFβ), a powerful signaling molecule that, when overactive, causes damaging scar tissue buildup.
#MolecularBiology #StructuralBiology #Biochemistry #sflorg
https://www.sflorg.com/2026/08/mbio08052601.html

Researchers have uncovered how a specific protein, latent TGFβ-binding protein 1 (LTBP1), regulates and stabilizes transforming growth factor beta (TGFβ), a powerful signaling molecule that, when overactive, causes damaging scar tissue buildup.
#MolecularBiology #StructuralBiology #Biochemistry #sflorg
https://www.sflorg.com/2026/08/mbio08052601.html

New Title Alert: Leopard-EM (Location & oriEntatiOn of PARticles found using two-Dimensional tEmplate Matching) is a python package for running two-dimensional template matching (2DTM) on cryo-EM images.

More here: https://lucaslab-berkeley.github.io/Leopard-EM/

#SBGrid #Software #StructuralBiology

We finished our 2025-2026 Software Webinar season in July with a presentation from Mart So-Last on Ais, Pom, and easymode. In case you missed it, you can find the recorded version on the SBGridTV YouTube channel:

https://www.youtube.com/watch?v=YpZ2G2TpLLA

#Webinars #SBGrid #StructuralBiology

A novel methodology that utilizes flexible, single-stranded DNA as a programmable molecular glue to intentionally direct proteins into highly ordered, diffraction-quality crystals.
#StructuralBiology #Nanotechnology #Chemistry #Biochemistry #MaterialsScience #sflorg
https://www.sflorg.com/2026/07/bio07302601.html

A novel methodology that utilizes flexible, single-stranded DNA as a programmable molecular glue to intentionally direct proteins into highly ordered, diffraction-quality crystals.
#StructuralBiology #Nanotechnology #Chemistry #Biochemistry #MaterialsScience #sflorg
https://www.sflorg.com/2026/07/bio07302601.html

Researchers have identified two novel mechanisms by which the widely used antibiotic doxycycline inhibits bacterial protein synthesis, effectively halting bacterial growth and reproduction.
#MolecularBiology #Microbiology #Pharmacology #StructuralBiology #sflorg
https://www.sflorg.com/2026/07/mbio07282601.html

Researchers have identified two novel mechanisms by which the widely used antibiotic doxycycline inhibits bacterial protein synthesis, effectively halting bacterial growth and reproduction.
#MolecularBiology #Microbiology #Pharmacology #StructuralBiology #sflorg
https://www.sflorg.com/2026/07/mbio07282601.html

Lab Manager / Research Associate -- Joiner Lab, Univ. of Cincinnati
University of Cincinnati

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-cincinnati-27778-lab-manager-research-associate-joiner-lab-univ-of-cincinnati/

#biochemistry #cellbiology #structuralbiology #ScienceJobs #hiring #research
https://jobrxiv.org/job/university-of-cincinnati-27778-lab-manager-research-associate-joiner-lab-univ-of-cincinnati/?fsp_sid=13944

Lab Manager / Research Associate -- Joiner Lab, Univ. of Cincinnati
University of Cincinnati

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-cincinnati-27778-lab-manager-research-associate-joiner-lab-univ-of-cincinnati/

#biochemistry #cellbiology #structuralbiology #ScienceJobs #hiring #research
https://jobrxiv.org/job/university-of-cincinnati-27778-lab-manager-research-associate-joiner-lab-univ-of-cincinnati/?fsp_sid=13944

An asymmetric structural conformation of the BRAF protein that forms during cellular signaling cascades and is responsible for driving uncontrolled cell division in certain cancers when the protein is mutated.
#MolecularBiology #StructuralBiology #Oncology #sflorg
https://www.sflorg.com/2026/07/mbio07212601.html

An asymmetric structural conformation of the BRAF protein that forms during cellular signaling cascades and is responsible for driving uncontrolled cell division in certain cancers when the protein is mutated.
#MolecularBiology #StructuralBiology #Oncology #sflorg
https://www.sflorg.com/2026/07/mbio07212601.html

Researchers have successfully mapped six major conformations of human acid-sensing ion channel 1a (ASIC1a), a critical brain membrane protein associated with learning, memory, fear-related behavior, and stroke-induced tissue damage.
#StructuralBiology #MolecularNeuroscience #Pharmacology #sflorg
https://www.sflorg.com/2026/07/bio07162601.html

Researchers have successfully mapped six major conformations of human acid-sensing ion channel 1a (ASIC1a), a critical brain membrane protein associated with learning, memory, fear-related behavior, and stroke-induced tissue damage.
#StructuralBiology #MolecularNeuroscience #Pharmacology #sflorg
https://www.sflorg.com/2026/07/bio07162601.html

Technical Notes: June's software push includes updates to 15 titles -- AlphaFold3, AlphaPulldown, ChemEx, cryoDRGN, DeepDeWedge, EMReady2, OpenForceField Toolkit, MassiveFold, ModelAngelo, PRODIGY, PowerFit, protein-quest, Scipion, STOPGAP, and TOMOMAN.

More here: https://sbgrid.org/software/recent/archive/2026/06/

#SBGrid #Software #StructuralBiology

Kinesin-1 is a highly specialized motor protein that sustains nerve cells by hauling vital cargo, such as packages of neurotransmitters, from the cellular center to the distant tips of the cell's branches.
#MolecularBiology #CellBiology #StructuralBiology #Neurobiology #sflorg
https://www.sflorg.com/2026/07/mbio07152601.html

Kinesin-1 is a highly specialized motor protein that sustains nerve cells by hauling vital cargo, such as packages of neurotransmitters, from the cellular center to the distant tips of the cell's branches.
#MolecularBiology #CellBiology #StructuralBiology #Neurobiology #sflorg
https://www.sflorg.com/2026/07/mbio07152601.html

Join us July 14th for the last in this season's software webinars with a presentation on the cryo-ET tools Ais and Pom from Mart So-Last of the Allegretti group at MRC Laboratory of Molecular Biology (LMB).

Tues, July 14, 2026 - 12:00pm ET
Ais and Pom

Register here: https://sbgrid.org/webinars/

#Webinars #SBGrid #StructuralBiology

Bacterial membrane protein insertion is the complex biochemical process by which newly synthesized hydrophobic proteins are transported from ribosomes and correctly folded into the cell membrane.
#Biochemistry #MolecularBiology #StructuralBiology #Microbiology #sflorg
https://www.sflorg.com/2026/06/bchem06292601.html

Bacterial membrane protein insertion is the complex biochemical process by which newly synthesized hydrophobic proteins are transported from ribosomes and correctly folded into the cell membrane.
#Biochemistry #MolecularBiology #StructuralBiology #Microbiology #sflorg
https://www.sflorg.com/2026/06/bchem06292601.html

Postdoctoral Researcher – Single-Molecule Biophysics/Structural Biology
The University of Texas at Austin

We are hiring a #StructuralBiology postdoc to study real-time membrane protein dynamics using high-speed AFM.

See the full job description on jobRxiv: https://jobrxiv.org/job/the-university-of-texas-at-austin-27778-postdoctoral-researcher-...
https://jobrxiv.org/job/the-university-of-texas-at-austin-27778-postdoctoral-researcher-single-molecule-biophysics-structural-biology/?fsp_sid=13243

Postdoctoral Researcher – Single-Molecule Biophysics/Structural Biology
The University of Texas at Austin

We are hiring a #StructuralBiology postdoc to study real-time membrane protein dynamics using high-speed AFM.

See the full job description on jobRxiv: https://jobrxiv.org/job/the-university-of-texas-at-austin-27778-postdoctoral-researcher-...
https://jobrxiv.org/job/the-university-of-texas-at-austin-27778-postdoctoral-researcher-single-molecule-biophysics-structural-biology/?fsp_sid=13243

11-Jun-2026
#Collagen, the human body’s most abundant #protein, is liquid-like inside #cells
New study overturns a 60-year-old assumption about the body's primary structural building block, opening new avenues for treating fibrosis and cancer.

https://www.eurekalert.org/news-releases/1131325

#science #nanoworld #structuralBiology

11-Jun-2026
#Collagen, the human body’s most abundant #protein, is liquid-like inside #cells
New study overturns a 60-year-old assumption about the body's primary structural building block, opening new avenues for treating fibrosis and cancer.

https://www.eurekalert.org/news-releases/1131325

#science #nanoworld #structuralBiology

Technical Notes: May's software push includes updates to AlphaFold3, autoPROC, BoltzGen, Buster, CCP4, ChemEx, COOT, cryoCAT , DIALS, Maxit, MotionCor3, OpenFreeEnergy, OpenMM, PowerFit, pytom-match-pick, TOMOMAN, Topaz, Volume_Seg_Tool, and Warp.

More here: https://sbgrid.org/software/recent/archive/2026/05/

#SBGrid #StructuralBiology #Software

🧬 If structure determines function, how can we optimize DNA therapeutics without accurately predicting their 3D shape?

🔗 Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0127

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#StructuralBiology #DNA #ComputationalBiology #Bioinformatics #MolecularBiology #Aptamers #DNANanotechnology #GenomeEngineering #NucleicAcids

🧬 If structure determines function, how can we optimize DNA therapeutics without accurately predicting their 3D shape?

🔗 Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0127

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#StructuralBiology #DNA #ComputationalBiology #Bioinformatics #MolecularBiology #Aptamers #DNANanotechnology #GenomeEngineering #NucleicAcids

The GluK2/GluK5 kainate receptor heteromer is a specialized ionotropic glutamate receptor complex in the brain, composed of two GluK2 and two GluK5 subunits, that functions as a glutamate-activated ion channel to transmit excitatory neuronal signals.
#CellularNeurobiology #StructuralBiology #Biochemistry #Biophysics #sflorg
https://www.sflorg.com/2026/06/cbio06082601.html

The GluK2/GluK5 kainate receptor heteromer is a specialized ionotropic glutamate receptor complex in the brain, composed of two GluK2 and two GluK5 subunits, that functions as a glutamate-activated ion channel to transmit excitatory neuronal signals.
#CellularNeurobiology #StructuralBiology #Biochemistry #Biophysics #sflorg
https://www.sflorg.com/2026/06/cbio06082601.html

Postdoc Positions - Structural Biology, Biochemistry, Cell Biology
University of Cincinnati

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-cincinnati-27778-postdoc-positions-structural-biology-biochemistry-cell-biology/

#biochemistry #cellbiology #cryoEM #proteinbiochemistry #structuralbiology #ScienceJobs #hiring #research
https://jobrxiv.org/job/university-of-cincinnati-27778-postdoc-positions-structural-biology-biochemistry-cell-biology/?fsp_sid=12578

Postdoc Positions - Structural Biology, Biochemistry, Cell Biology
University of Cincinnati

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-cincinnati-27778-postdoc-positions-structural-biology-biochemistry-cell-biology/

#biochemistry #cellbiology #cryoEM #proteinbiochemistry #structuralbiology #ScienceJobs #hiring #research
https://jobrxiv.org/job/university-of-cincinnati-27778-postdoc-positions-structural-biology-biochemistry-cell-biology/?fsp_sid=12578

Molecular & Structural Biology Scientist (Internship to Hire)
BalanX Bio

See the full job description on jobRxiv: https://jobrxiv.org/job/balanx-bio-27779-molecular-structural-biology-scientist/

#cryoEM #structuralbiology #ScienceJobs #hiring #research
https://jobrxiv.org/job/balanx-bio-27779-molecular-structural-biology-scientist/?fsp_sid=12507

Molecular & Structural Biology Scientist (Internship to Hire)
BalanX Bio

See the full job description on jobRxiv: https://jobrxiv.org/job/balanx-bio-27779-molecular-structural-biology-scientist/

#cryoEM #structuralbiology #ScienceJobs #hiring #research
https://jobrxiv.org/job/balanx-bio-27779-molecular-structural-biology-scientist/?fsp_sid=12507

People of the Fediverse! I have accomplished science. Allow me to elaborate...

"Discovery of a sulfotyrosine-motif in the human TrkB extracellular domain
required for agonist activation"

https://www.biorxiv.org/content/10.64898/2026.05.19.725324v1

#Science #Neurobiology #StructuralBiology #Biochemistry #Pharmacology #SeeMyScience #OpenScience

People of the Fediverse! I have accomplished science. Allow me to elaborate...

"Discovery of a sulfotyrosine-motif in the human TrkB extracellular domain
required for agonist activation"

https://www.biorxiv.org/content/10.64898/2026.05.19.725324v1

#Science #Neurobiology #StructuralBiology #Biochemistry #Pharmacology #SeeMyScience #OpenScience

🦠 Could decoding bacterial regulatory proteins help us stay ahead of drug resistance?

🔗 Conserved Motifs in the Ligand-Binding Domain of TetR Family Regulators: Identification and Analysis. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0100

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#Microbiology #MolecularBiology #Bioinformatics #AntimicrobialResistance #DrugDiscovery #ProteinEngineering #StructuralBiology #Genomics #ComputationalBiology

🦠 Could decoding bacterial regulatory proteins help us stay ahead of drug resistance?

🔗 Conserved Motifs in the Ligand-Binding Domain of TetR Family Regulators: Identification and Analysis. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0100

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#Microbiology #MolecularBiology #Bioinformatics #AntimicrobialResistance #DrugDiscovery #ProteinEngineering #StructuralBiology #Genomics #ComputationalBiology

Plants utilize a specialized copper-dependent sensing system within their plasma membrane receptors to detect hydrogen peroxide (H₂O₂), a vital signaling molecule involved in stress responses and plant immunity.
#Botany #Biochemistry #MolecularBiology #StructuralBiology #sflorg
https://www.sflorg.com/2026/05/bot05212601.html

Plants utilize a specialized copper-dependent sensing system within their plasma membrane receptors to detect hydrogen peroxide (H₂O₂), a vital signaling molecule involved in stress responses and plant immunity.
#Botany #Biochemistry #MolecularBiology #StructuralBiology #sflorg
https://www.sflorg.com/2026/05/bot05212601.html

📢 We are pleased to announce that authors can now submit manuscripts directly from bioRxiv to CSBJ through the 𝗯𝗶𝗼𝗥𝘅𝗶𝘃-𝘁𝗼-𝗝𝗼𝘂𝗿𝗻𝗮𝗹 (B2J) transfer service.

🙏We sincerely thank Cold Spring Harbor Laboratory (CSHL) for integrating CSBJ into the B2J service.

#CSBJ #bioRxiv #AAAS #OpenScience #Preprints #SystemsBiology #StructuralBiology #Biotechnology #ComputationalBiology #Omics #Nanoscience #MedicalInformatics #Biomedicine #AdvancedMaterials #Biomaterials #QuantumBiology #Biophotonics

RE: https://fediscience.org/@Guillawme/115798148618761432

This article on an ALC1-nucleosome complex with a new conformation was accepted at @ActaCrystD in April and went online today! Check it out!

https://doi.org/10.1107/S2059798326004158

#CryoEM #StructuralBiology #nucleosome #chromatin

Some days I feel like this RNA model I just made. A lot broken and twisting in mysterious ways.

#compchem #model #rna #structure #structuralbiology

Researchers have successfully characterized the first human antibodies capable of neutralizing the measles virus, providing the foundation for highly targeted prophylactic and post-exposure medical therapies.
#Immunology #Virology #StructuralBiology #sflorg
https://www.sflorg.com/2026/05/imgy05102601.html

⚛️ Can spherical voxelization improve how AI interprets protein chemistry and interactions?

🔗 SpheronizaTor: Spherical Voxelization for Interpretable Protein Microenvironment Modeling. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0076

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#StructuralBiology #Bioinformatics #ComputationalBiology #ProteinStructure #ArtificialIntelligence #ProteinEngineering #ProteinModeling

Lab Manager / Research Associate -- Joiner Lab, Univ. of Cincinnati
University of Cincinnati

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-cincinnati-27778-lab-manager-research-associate-joiner-lab-univ-of-cincinnati/

#biochemistry #cellbiology #structuralbiology #ScienceJobs #hiring #research
https://jobrxiv.org/job/university-of-cincinnati-27778-lab-manager-research-associate-joiner-lab-univ-of-cincinnati/?fsp_sid=11881