List of works - Khaled Barakat

A Comprehensive Computational Analysis for the Binding Modes of Hepatitis C Virus NS5A Inhibitors: The Question of Symmetry.

scientific article

A Novel Interaction Between the TLR7 and a Colchicine Derivative Revealed Through a Computational and Experimental Study.

scientific article published on 16 February 2018

A Refined Model of the HCV NS5A protein bound to daclatasvir explains drug-resistant mutations and activity against divergent genotypes.

scientific article published on 14 April 2014

A comprehensive structural model for the human KCNQ1/KCNE1 ion channel.

scientific article published on 29 September 2017

A computational model for overcoming drug resistance using selective dual-inhibitors for aurora kinase A and its T217D variant

scientific article published on 5 November 2013

A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity.

scientific article published on 13 August 2014

A mathematical modelling tool for unravelling the antibody-mediated effects on CTLA-4 interactions.

scientific article

An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions

scientific article

Applications of computer-aided approaches in the development of hepatitis C antiviral agents

scientific article

Atomistic modeling and molecular dynamics analysis of human CaV1.2 channel using external electric field and ion pulling simulations

scientific article published on 09 April 2019

Binding modes of hERG blockers: an unsolved mystery in the drug design arena

scientific article published on 14 December 2017

Characterization of an inhibitory dynamic pharmacophore for the ERCC1-XPA interaction using a combined molecular dynamics and virtual screening approach.

scientific article

Coinhibitory Receptor Expression and Immune Checkpoint Blockade: Maintaining a Balance in CD8+ T Cell Responses to Chronic Viral Infections and Cancer.

scientific article published on 29 September 2017

Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease.

scientific article published on 30 April 2018

Computational predictions of volatile anesthetic interactions with the microtubule cytoskeleton: implications for side effects of general anesthesia

scientific article

Cyclosporine A binding to COX-2 reveals a novel signaling pathway that activates the IRE1α unfolded protein response sensor

scientific article published in Scientific Reports

DNA polymerase beta (pol β) inhibitors: a comprehensive overview.

scientific article published on 25 April 2012

Design, synthesis, biological evaluation and dynamics simulation of indazole derivatives with antiangiogenic and antiproliferative anticancer activity

scientific article published on 02 November 2018

Detailed computational study of the active site of the hepatitis C viral RNA polymerase to aid novel drug design.

scientific article published on 24 October 2013

Development of Safe Drugs: The hERG Challenge.

scientific article published on 3 May 2017

Discovery of Novel Peptidomimetics as Irreversible CHIKV NsP2 Protease Inhibitors Using Quantum Mechanical-Based Ligand Descriptors

scientific article published on 25 July 2015

Discovery of Small Molecule Inhibitors that Interact with γ-Tubulin

scientific article published on 15 February 2012

Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel

scientific article published on 14 February 2018

Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: comparing the wild type to the R248Q mutant.

scientific article

Electrostatic contributions to colchicine binding within tubulin isotypes.

scientific article

Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions.

scientific article

Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods.

scientific article published on 15 September 2015

Human PD-1 binds differently to its human ligands: a comprehensive modeling study

scientific article published on 14 February 2015

Human structural proteome-wide characterization of Cyclosporine A targets

scientific article published on 28 August 2014

IL-28B is a key regulator of B- and T-cell vaccine responses against influenza

scientific article

Immunomodulatory Function of Interleukin 28B during primary infection with cytomegalovirus.

scientific article published on 11 March 2014

Modeling the human Nav1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade.

scientific article

Modeling the yew tree tubulin and a comparison of its interaction with paclitaxel to human tubulin.

scientific article published on 26 July 2012

Modelling DNA Repair Pathways: Recent Advances and Future Directions

scientific article published on 20 April 2016

Molecular Dynamics Simulation and Prediction of Druggable Binding Sites

scientific article published on 01 January 2018

Molecular dynamics-driven drug discovery: leaping forward with confidence

scientific article published on 24 November 2016

New design of nucleotide excision repair (NER) inhibitors for combination cancer therapy.

scientific article published on 26 February 2016

Novel Allosteric Pathway of Eg5 Regulation Identified through Multivariate Statistical Analysis of Hydrogen-Exchange Mass Spectrometry (HX-MS) Ligand Screening Data

scientific article

Phase transitions of methane using molecular dynamics simulations

scientific article published on 01 March 2006

Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta.

scientific article

Revealing the atomistic details behind the binding of B7-1 to CD28 and CTLA-4: A comprehensive protein-protein modelling study

scientific article published on 10 August 2018

Structure-based screening and validation of potential dengue virus inhibitors through classical and QM/MM affinity estimation

scientific article published on 24 April 2019

Targeting B7-1 in immunotherapy

scientific article published on 25 August 2019

Targeting the Achilles heel of the hepatitis B virus: a review of current treatments against covalently closed circular DNA.

scientific article

The Effect of Aflatoxin B1 on Tumor-Related Genes and Phenotypic Characters of MCF7 and MCF10A Cells

scientific article published in 2022

The Too Many Faces of PD-L1: A Comprehensive Conformational Analysis Study

scientific article published on 12 September 2017

Vaccine adjuvants--understanding molecular mechanisms to improve vaccines.

scientific article published on 20 May 2014

When theory meets experiment: the PD-1 challenge

scientific article published on 10 October 2017

List of works by Khaled Barakat

A Comprehensive Computational Analysis for the Binding Modes of Hepatitis C Virus NS5A Inhibitors: The Question of Symmetry.

A Novel Interaction Between the TLR7 and a Colchicine Derivative Revealed Through a Computational and Experimental Study.

A Refined Model of the HCV NS5A protein bound to daclatasvir explains drug-resistant mutations and activity against divergent genotypes.

A comprehensive structural model for the human KCNQ1/KCNE1 ion channel.

A computational model for overcoming drug resistance using selective dual-inhibitors for aurora kinase A and its T217D variant

A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity.

A mathematical modelling tool for unravelling the antibody-mediated effects on CTLA-4 interactions.

An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions

Applications of computer-aided approaches in the development of hepatitis C antiviral agents

Atomistic modeling and molecular dynamics analysis of human CaV1.2 channel using external electric field and ion pulling simulations

Binding modes of hERG blockers: an unsolved mystery in the drug design arena

Characterization of an inhibitory dynamic pharmacophore for the ERCC1-XPA interaction using a combined molecular dynamics and virtual screening approach.

Coinhibitory Receptor Expression and Immune Checkpoint Blockade: Maintaining a Balance in CD8+ T Cell Responses to Chronic Viral Infections and Cancer.

Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease.

Computational predictions of volatile anesthetic interactions with the microtubule cytoskeleton: implications for side effects of general anesthesia

Cyclosporine A binding to COX-2 reveals a novel signaling pathway that activates the IRE1α unfolded protein response sensor

DNA polymerase beta (pol β) inhibitors: a comprehensive overview.

Design, synthesis, biological evaluation and dynamics simulation of indazole derivatives with antiangiogenic and antiproliferative anticancer activity

Detailed computational study of the active site of the hepatitis C viral RNA polymerase to aid novel drug design.

Development of Safe Drugs: The hERG Challenge.

Discovery of Novel Peptidomimetics as Irreversible CHIKV NsP2 Protease Inhibitors Using Quantum Mechanical-Based Ligand Descriptors

Discovery of Small Molecule Inhibitors that Interact with γ-Tubulin

Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel

Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: comparing the wild type to the R248Q mutant.

Electrostatic contributions to colchicine binding within tubulin isotypes.

Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions.

Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods.

Human PD-1 binds differently to its human ligands: a comprehensive modeling study

Human structural proteome-wide characterization of Cyclosporine A targets

IL-28B is a key regulator of B- and T-cell vaccine responses against influenza

Immunomodulatory Function of Interleukin 28B during primary infection with cytomegalovirus.

Modeling the human Nav1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade.

Modeling the yew tree tubulin and a comparison of its interaction with paclitaxel to human tubulin.

Modelling DNA Repair Pathways: Recent Advances and Future Directions

Molecular Dynamics Simulation and Prediction of Druggable Binding Sites

Molecular dynamics-driven drug discovery: leaping forward with confidence

New design of nucleotide excision repair (NER) inhibitors for combination cancer therapy.

Novel Allosteric Pathway of Eg5 Regulation Identified through Multivariate Statistical Analysis of Hydrogen-Exchange Mass Spectrometry (HX-MS) Ligand Screening Data

Phase transitions of methane using molecular dynamics simulations

Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta.

Revealing the atomistic details behind the binding of B7-1 to CD28 and CTLA-4: A comprehensive protein-protein modelling study

Structure-based screening and validation of potential dengue virus inhibitors through classical and QM/MM affinity estimation

Targeting B7-1 in immunotherapy

Targeting the Achilles heel of the hepatitis B virus: a review of current treatments against covalently closed circular DNA.

The Effect of Aflatoxin B1 on Tumor-Related Genes and Phenotypic Characters of MCF7 and MCF10A Cells

The Too Many Faces of PD-L1: A Comprehensive Conformational Analysis Study

Vaccine adjuvants--understanding molecular mechanisms to improve vaccines.

When theory meets experiment: the PD-1 challenge