Alper Karagöl

The paper identifies two opposite failure modes in alignment-based conservation scores and shows how to correct them to improve score accuracy.

This paper converts the N-terminal bundle of Apolipoprotein E to be membrane-compatible using reverse-QTY substitutions without altering its fold, demonstrating preserved helix content and increased hydrophobicity.

This paper introduces Dynamics-Aware Evolutionary Profiling to separate structural rigidity from functional motion in proteins, improving variant interpretation by identifying dynamic-conserved residues.

The paper systematically analyzes the structural impact of proteolytic truncation on human homodimers, identifying two rules governing interface preservation and emergence.

The paper uses simulations to show a truncated NET isoform disrupts MAT bio-assembly by forming non-native heterodimers and causing structural instability.

The paper introduces Tν, a metric to quantify directional asymmetry in amino acid substitutions using kernel regression on MSAs, and applies it to human glutamate transporters to identify high-tension sites and pathogenic variants.

The paper identifies a truncated VMAT1 splice isoform that inhibits canonical VMAT oligomerization through altered binding affinity and charge interactions.

This study investigates how isoelectric point (pI) influences evolutionary residue selection and structural stability in JAM paralogs through integrated analysis of conservation, dynamics, and pathogenicity.

The paper identifies a conserved motif linked to β-sheet oligomerization in EAA1 isoforms through evolutionary analysis of helix-to-sheet transitions across species.

The paper characterizes truncated isoforms of the glutamate transporter EAA1, showing they self-assemble into β-sheet oligomers and may contribute to neurodegeneration.

This study investigates how pH changes affect synaptogyrin-1 and -3 behavior, revealing their distinct responses and implications for synaptic function and neurodegenerative diseases.

This study compares the evolutionary adaptation of membrane-bound and soluble TLR5 forms in orange-spotted grouper to understand their solubility and structural differences.

This work benchmarks GROMACS on Google Colab processors, highlighting performance improvements and limitations for molecular dynamics simulations.

The paper introduces an open-source web-based toolkit for evolutionary sequence analysis, offering multiple statistical tools and educational resources.