Virtual Screening: An Overview on Methods and Applications. - Khaled H. Barakat; Jonathan Y. Mane; Jack A. Tuszynski (Handbook of Research on Computational and Systems Biology, 2011)

Detailed Computational Study of the Active Site of the Hepatitis C Viral RNA Polymerase to Aid Novel Drug Design. - Khaled H. Barakat; John Law; Alessio Prunotto; Wendy C. Magee; David H. Evans 002; D. Lorne Tyrrell; Jack A. Tuszynski; Michael Houghton (J. Chem. Inf. Model., 2013)

Human structural proteome-wide characterization of Cyclosporine A targets. - Gang Hu; Kui Wang; Jody Groenendyk; Khaled H. Barakat; Marcin J. Mizianty; Jishou Ruan; Marek Michalak; Lukasz A. Kurgan (Bioinform., 2014)

Rational Drug Design: One Target, Many Paths to It. - Khaled H. Barakat; Michael Houghton; D. Lorne Tyrrell; Jack A. Tuszynski (Int. J. Comput. Model. Algorithms Medicine, 2014)

A Refined Model of the HCV NS5A Protein Bound to Daclatasvir Explains Drug-Resistant Mutations and Activity against Divergent Genotypes. - Khaled H. Barakat; Anwar Anwar-Mohamed; Jack A. Tuszynski; Morris J. Robins; D. Lorne Tyrrell; Michael Houghton (J. Chem. Inf. Model., 2015)

A mathematical modelling tool for unravelling the antibody-mediated effects on CTLA-4 interactions. - Aravindhan Ganesan; Theinmozhi Arulraj; Tahir Choulli; Khaled H. Barakat (BMC Medical Informatics Decis. Mak., 2018)

GRP78: A possible relationship of COVID-19 and the mucormycosis; in silico perspective. - Alaa M. Elgohary; Abdo A. Elfiky; Khaled H. Barakat (Comput. Biol. Medicine, 2021)

ToxTree: descriptor-based machine learning models for both hERG and Nav1.5 cardiotoxicity liability predictions. - Issar Arab; Khaled H. Barakat (CoRR, 2021)

Discovery of allosteric SHP2 inhibitors through ensemble-based consensus molecular docking, endpoint and absolute binding free energy calculations. - Maryam Jama; Marawan Ahmed; Anna Jutla; Carson Wiethan; Jitendra Kumar; Tae Chul Moon; Frederick West; Michael Overduin; Khaled H. Barakat (Comput. Biol. Medicine, 2023)

Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction. - Issar Arab; Kristof Egghe; Kris Laukens; Ke Chen; Khaled H. Barakat; Wout Bittremieux (J. Chem. Inf. Model., 2024)

Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch Using Well-Tempered Metadynamics Simulations. - Farag E. S. Mosa; Sara Alrawashdeh; Ayman O. S. El-Kadi; Khaled H. Barakat (J. Chem. Inf. Model., 2024)

Designing a multi-neoantigen vaccine for melanoma: Integrating immunoinformatics and biophysics methods. - Saba Ismail; Khaled H. Barakat (Comput. Biol. Medicine, 2025)