Andrej Šali

The paper shows hydrophobic FG-nucleoporins dilate nuclear pores during mitosis, enabling nuclear import and NE reformation.

This paper expands structural surfaceomics to identify cancer-specific protein conformations across multiple tumor models, revealing potential immunotherapy targets through crosslinking mass spectrometry and structural modeling.

The paper investigates how the ultrastructure of biomolecular condensates, using PopZ as a model, influences their function through molecular interactions and phase-dependent conformational changes.

The paper constructs an integrative Brownian dynamics model of nucleocytoplasmic transport, revealing how FG repeat proteins and nuclear transport receptors mediate selective transport through NPCs.

The paper analyzes the structural and dynamic differences between ChikV Mac1 and SARS-CoV-2 Mac1 to explain differences in ligand binding affinity and designs inhibitors for ChikV Mac1.

The paper develops MultiXray, a Bayesian method for multi-state and multi-condition protein structure modeling using X-ray crystallography data, improving Rfree values in both simulated and experimental cases.

AlphaCross-XL automates mapping of crosslinked peptides to protein structures at proteome scale, enabling analysis of thousands of proteins.

EMSequenceFinder accurately assigns amino acid sequences to cryo-EM map backbone fragments, outperforming existing methods in resolution 3-10 Å maps.

This study identifies the structural and sequence basis of epistatic interactions driving drug resistance in HIV by combining sequence models and molecular dynamics simulations.

This study identifies two inhibitors of the Mtb efflux pump EfpA, determines their binding mechanisms, and suggests their potential for combination anti-tuberculosis therapy.

The paper introduces an integrative spatiotemporal modeling method for dynamic biomolecular processes, applied to Nuclear Pore Complex assembly, improving model precision over static approaches.

This study identifies mechanisms enabling nanobodies to bind antigens with high affinity and stability, revealing a conserved region critical for their function and suggesting strategies for their optimization.

This study uses structural biology to reveal the architecture of the nuclear basket in yeast and mammals, showing how Mlp/Tpr proteins form its structural components.

The paper introduces a multi-scale proximity labeling method using Eosin Y to map cell surface protein neighborhoods at varying resolutions and validates interactions of EGFR and CAR-T cell synapses.

This study identifies SLC22A10 as a nonfunctional pseudogene in humans due to a missense mutation, while great ape orthologs retain functional uptake of estradiol-17β-glucuronide.

The paper introduces the CM4AI project, which aims to create AI-ready datasets of human cell architecture using multimodal data from cell lines.

The paper shows that nanobodies against ancestral SARS-CoV-2 spike protein remain effective against recent variants, including omicron sublineages and emerging XBB/BQ.1.1 variants.

The paper introduces BFF, a Bayesian framework for processing fluorescence data to improve biomolecular modeling accuracy and precision using synthetic single-molecule FRET data.

ModelCIF extends the PDBx/mmCIF standard to represent predicted 3D protein models, enabling FAIR data sharing for computational structural biology.

The paper presents an integrative structural analysis of the Smc5/6 complex in budding yeast, revealing unique structural features and functional interactions among its subunits.

This paper introduces ITCell, a method that predicts CD4 T-cell epitopes by integrating antigen cleavage, MHCII presentation, and TCR recognition, achieving higher accuracy than single-stage methods.

The paper introduces a Bayesian scoring function to rank structural models using cryo-EM data and other information, validated on known complexes and implemented in an open-source platform.