Collective Behavior of el Farol Attendees. - Canan Atilgan; Ali Rana Atilgan; Güven Demirel (Adv. Complex Syst., 2008)

Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein. - Canan Atilgan; Ali Rana Atilgan (PLoS Comput. Biol., 2009)

Assortative Mixing in Close-Packed Spatial Networks - Deniz Turgut; Ali Rana Atilgan; Canan Atilgan (CoRR, 2010)

Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin. - Ayse Ozlem Aykut; Ali Rana Atilgan; Canan Atilgan (PLoS Comput. Biol., 2013)

MD-TASK: a software suite for analyzing molecular dynamics trajectories. - David K. Brown; David L. Penkler; Olivier Sheik Amamuddy; Caroline J. Ross; Ali Rana Atilgan; Canan Atilgan; Özlem Tastan Bishop (Bioinform., 2017)

Perturbation-Response Scanning Reveals Key Residues for Allosteric Control in Hsp70. - David L. Penkler; Özge Sensoy; Canan Atilgan; Özlem Tastan Bishop (J. Chem. Inf. Model., 2017)

MODE-TASK: large-scale protein motion tools. - Caroline J. Ross; Bilal Nizami; Michael Glenister; Olivier Sheik Amamuddy; Ali Rana Atilgan; Canan Atilgan; Özlem Tastan Bishop (Bioinform., 2018)

Allosteric Modulation of Human Hsp90α Conformational Dynamics. - David L. Penkler; Canan Atilgan; Özlem Tastan Bishop (J. Chem. Inf. Model., 2018)

Tuning Interaction Parameters of Thermoplastic Polyurethanes in a Binary Solvent To Achieve Precise Control over Microphase Separation. - Senem Avaz Seven; Oguzhan Oguz; Yusuf Ziya Menceloglu; Canan Atilgan (J. Chem. Inf. Model., 2019)

Could network structures generated with simple rules imposed on a cubic lattice reproduce the structural descriptors of globular proteins? - Osman Burak Okan; Deniz Turgut; Canan Atilgan; Ali Rana Atilgan; Rahmi Ozisik (J. Complex Networks, 2021)

N-Terminus of the Third PDZ Domain of PSD-95 Orchestrates Allosteric Communication for Selective Ligand Binding. - Tandac F. Guclu; Nazli Kocatug; Ali Rana Atilgan; Canan Atilgan (J. Chem. Inf. Model., 2021)

DHFR Mutants Modulate Their Synchronized Dynamics with the Substrate by Shifting Hydrogen Bond Occupancies. - Ebru Çetin; Ali Rana Atilgan; Canan Atilgan (J. Chem. Inf. Model., 2022)

Nonlocal Effects of Antibiotic-Resistance-Causing Mutations Reveal an Alternative Region for Targeting on FtsW-Penicillin-Binding Protein 3 Complex of Haemophilus influenzae. - Almotasem Belah Alhamwi; Canan Atilgan; Özge Sensoy (J. Chem. Inf. Model., 2023)

Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR. - Ebru Çetin; Tandac F. Guclu; Isik Kantarcioglu; Ilona K. Gaszek; Erdal Toprak; Ali Rana Atilgan; Burcu Dedeoglu; Canan Atilgan (J. Chem. Inf. Model., 2023)

Ranking Single Fluorescent Protein-Based Calcium Biosensor Performance by Molecular Dynamics Simulations. - Melike Berksoz; Canan Atilgan (J. Chem. Inf. Model., 2025)

High Throughput Mutational Scanning of a Protein via Alchemistry on a High-Performance Computing Resource. - Tandac F. Guclu; Busra Tayhan; Ebru Çetin; Ali Rana Atilgan; Canan Atilgan (Concurr. Comput. Pract. Exp., 2025)