Anastassis Perrakis A

The paper develops a validated TCR-pMHC database (TCRvdb) by assessing VDJdb entries with a high-throughput platform, finding only 50% of claims are functionally confirmed.

AlphaBridge evaluates predicted biomolecular complexes using AlphaFold3 confidence metrics, clustering sequence motifs, and visualizing interfaces with 2D diagrams and interactive tools.

This study investigates the functional divergence between two macro domains in PARP9, showing how their distinct thermodynamics and ligand binding dynamics enable their roles as an eraser and a reader.

The paper analyzes halogen bonds in protein-ligand complexes using geometric parameters and introduces a score to assess their validity in structure models from PDB-REDO.

The paper constructs an atlas of human multi-protein complexes by integrating computational structure predictions with genetic dependency data, identifying 354 high-confidence complexes including novel ones.

DSSP 4 annotates protein secondary structure in a FAIR-compliant manner, introducing left-handed κ-helices and improving interoperability with mmCIF format.

The paper identifies M18BP1 as a factor required for condensin II localization to chromatin and shows it competes with MCPH1 to activate condensin II during mitosis.

The paper develops a comprehensive dataset of intrinsic disorder in human proteins, revealing that most proteins contain disordered regions with distinct characteristics and pathogenic mutation risks.

This study identifies Caskin2 as a novel talin-binding protein that enhances cell motility through interactions with Abi1 and the WAVE Regulatory Complex.

The paper investigates structural plasticity in Parechovirus 2A proteins, revealing structural rearrangements that affect their oligomeric state and potential function in viral RNA replication.

AlphaFill adds missing ligands and cofactors to AlphaFold protein models using sequence and structure similarity to improve functional interpretation.

This study evaluates a type IV ATX inhibitor, Cpd17, showing improved efficacy over a type I inhibitor in reducing liver injury in mouse models of acute liver injury and non-alcoholic steatohepatitis.

This study identifies sequence-dependent trafficking pathways of GDE2 that regulate its function in neuronal differentiation and neurodegeneration.

The paper shows that Cdt2 binds PCNA via a PIP box, enhancing CRL4Cdt2 activity and Cdt1 ubiquitination, suggesting a new mechanism for substrate targeting.

The paper presents methods to complete missing regions in protein structures using homology information, resulting in 24,962 completed loops in the PDB.

This study shows that GDE2 regulates pancreas differentiation in zebrafish by affecting Notch signaling, with functional conservation between zebrafish and human GDE2.