Orly Avraham
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View article: Protein language models can capture protein quaternary state
Protein language models can capture protein quaternary state Open
View article: Protein language models can capture protein quaternary state
Protein language models can capture protein quaternary state Open
Background: Determining a protein’s quaternary state, i.e. the number of monomers in a functional unit, is a critical step in protein characterization. Many proteins form multimers for their activity, and over 50% are estimated to naturall…
View article: Protein language models can capture protein quaternary state
Protein language models can capture protein quaternary state Open
Background Determining a protein’s quaternary state, i.e . how many monomers assemble together to form the functioning unit, is a critical step in protein characterization, and deducing it is not trivial. Many proteins form multimers for t…
View article: Additional file 1 of Protein language models can capture protein quaternary state
Additional file 1 of Protein language models can capture protein quaternary state Open
Additional file 1: Supplementary Table SI: Embeddings.
View article: Structural insights into the role of the WW2 domain on tandem WW–PPxY motif interactions of oxidoreductase WWOX
Structural insights into the role of the WW2 domain on tandem WW–PPxY motif interactions of oxidoreductase WWOX Open
View article: Matching protein surface structural patches for high-resolution blind peptide docking
Matching protein surface structural patches for high-resolution blind peptide docking Open
Significance Modeling interactions between short peptides and their receptors is a challenging docking problem due to the peptide flexibility, resulting in a formidable sampling problem of peptide conformation in addition to its orientatio…
View article: Eine vielseitige synthetische Affinitätssonde zur hochaufgelösten Visualisierung hemmender Synapsen und neuronaler Netzwerke**
Eine vielseitige synthetische Affinitätssonde zur hochaufgelösten Visualisierung hemmender Synapsen und neuronaler Netzwerke** Open
Die Visualisierung von inhibitorischen Synapsen erfordert auf Sondentypen und das jeweilige bildgebende Verfahren abgestimmte Protokolle und beruht in der Regel auf genetischer Manipulation oder der Verwendung von Antikörpern, die bei Gewe…
View article: A Versatile Synthetic Affinity Probe Reveals Inhibitory Synapse Ultrastructure and Brain Connectivity**
A Versatile Synthetic Affinity Probe Reveals Inhibitory Synapse Ultrastructure and Brain Connectivity** Open
Visualization of inhibitory synapses requires protocol tailoring for different sample types and imaging techniques, and usually relies on genetic manipulation or the use of antibodies that underperform in tissue immunofluorescence. Startin…
View article: Harnessing protein folding neural networks for peptide–protein docking
Harnessing protein folding neural networks for peptide–protein docking Open
View article: Tandem WW/PPxY motif interactions in WWOX: the multifaceted role of the second WW domain
Tandem WW/PPxY motif interactions in WWOX: the multifaceted role of the second WW domain Open
Class I WW domains mediate protein interactions by binding short linear PPxY motifs. They occur predominantly as tandem repeats, and their target proteins often contain multiple PPxY motifs, but the interplay of WW/peptide interactions is …
View article: Wilavidin* — a novel member of the avidin family that forms unique biotin‐binding hexamers
Wilavidin* — a novel member of the avidin family that forms unique biotin‐binding hexamers Open
Nature's optimization of protein functions is a highly intricate evolutionary process. In addition to optimal tertiary folding, the intramolecular recognition among the monomers that generate higher‐order quaternary arrangements is driven …
View article: PatchMAN docking: Modeling peptide-protein interactions in the context of the receptor surface
PatchMAN docking: Modeling peptide-protein interactions in the context of the receptor surface Open
Peptide docking can be perceived as a subproblem of protein-protein docking. However, due to the short length and flexible nature of peptides, many do not adopt one defined conformation prior to binding. Therefore, to tackle a peptide dock…
View article: Harnessing protein folding neural networks for peptide-protein docking
Harnessing protein folding neural networks for peptide-protein docking Open
Highly accurate protein structure predictions by the recently published deep neural networks such as AlphaFold2 and RoseTTAFold are truly impressive achievements, and will have a tremendous impact far beyond structural biology. If peptide-…
View article: Harnessing protein folding neural networks for peptide-protein docking
Harnessing protein folding neural networks for peptide-protein docking Open
Highly accurate protein structure predictions by the recently published deep neural networks such as AlphaFold2 and RoseTTAFold are truly impressive achievements, and will have a tremendous impact far beyond structural biology. If peptide-…
View article: Sylites: Multipurpose markers for the visualization of inhibitory synapses
Sylites: Multipurpose markers for the visualization of inhibitory synapses Open
We introduce Sylites – small and versatile fluorogenic affinity probes for high-contrast visualization of inhibitory synapses. Having stoichiometric labeling and exceptional selectivity for neuronal gephyrin, a hallmark protein of the inhi…
View article: Generating a High Valency Biotin Binder by Selecting Uniform Protein Assemblies via Crystallization
Generating a High Valency Biotin Binder by Selecting Uniform Protein Assemblies via Crystallization Open
Crystallization is a common practice in the purification process in small molecule synthesis while selecting the wanted product. For proteins it is rarely applied due to the methodological predicaments in obtaining crystals. Our observatio…
View article: Publisher Correction: Coupling Multi Angle Light Scattering to Ion Exchange chromatography (IEX-MALS) for protein characterization
Publisher Correction: Coupling Multi Angle Light Scattering to Ion Exchange chromatography (IEX-MALS) for protein characterization Open
View article: Crystal structure of afifavidin reveals common features of molecular assemblage in the bacterial dimeric avidins
Crystal structure of afifavidin reveals common features of molecular assemblage in the bacterial dimeric avidins Open
The subfamily of bacterial dimeric avidins is being extended through the discovery of additional members originating from diverse sources. All of these newly discovered dimeric avidin forms exhibit high affinity towards biotin, despite the…
View article: Coupling Multi Angle Light Scattering to Ion Exchange chromatography (IEX-MALS) for protein characterization
Coupling Multi Angle Light Scattering to Ion Exchange chromatography (IEX-MALS) for protein characterization Open
Multi-angle light scattering coupled with size exclusion chromatography (SEC-MALS) is a standard and common approach for characterizing protein mass, overall shape, aggregation, oligomerization, interactions and purity. The limited resolut…