Ezgi Karaca

DynaPIN extracts dynamic interface fingerprints from molecular simulations to better characterize protein interactions beyond static models.

The paper evaluates if AlphaFold distograms can predict binding-induced hinge motions in proteins, showing they capture flexibility not seen in predicted structures.

This study uses long-read RNA sequencing to uncover E2-regulated transcriptome complexity, revealing novel isoforms and truncated proteins with functional implications in ER+ breast cancer.

This study compares DNMT3A and DNMT3B to show how they recognize different flanking sequences through distinct mechanisms.

The paper shows that Fgf3 in zebrafish lateral line organogenesis represses target genes through nuclear accumulation, distinct from its extracellular signaling role.

The paper identifies AIFM1/AK2 interaction as a gatekeeper of mitochondrial ATP synthase, showing it is NADH-dependent and linked to metabolic state, with implications for mitochondrial diseases.

The paper applies enhanced AlphaFold2 sampling and data-driven docking to predict antibody-peptide and antibody-MHC I complexes, achieving medium-quality predictions for some targets.

The paper compares AlphaFold2 and AlphaFold3 predictions for human-parasite domain-domain interactions, finding significant differences in confidence scores.

The paper benchmarks six structure-based binding affinity predictors on Spike-ACE2 mutations, finding FoldX performs best with R = -0.51 and 64% accuracy in binary classification.

The paper evaluates AI-based protein assembly prediction in CASP15, showing improved performance over CASP14, with community models outperforming the baseline AF2-Multimer in many cases.

The paper evaluates sequence- and structure-based methods to predict specificity-determining positions in Axl complexes, finding sequence-based methods overpredict and that combining them with HADDOCK improves predictions.

The paper evaluates six web-based tools for predicting kinase mutation effects on ligand binding using a benchmark dataset, finding that some tools perform well when assessing directional changes in binding affinity.