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Items: 22

1.

Computer-Aided Drug Design of Small Molecule Inhibitors of the ERCC1-XPF Protein-Protein Interaction.

Gentile F, Elmenoufy AH, Ciniero G, Jay D, Karimi-Busheri F, Barakat KH, Weinfeld M, West FG, Tuszynski JA.

Chem Biol Drug Des. 2019 Dec 31. doi: 10.1111/cbdd.13660. [Epub ahead of print]

PMID:
31891209
2.

Targeting DNA Repair in Tumor Cells via Inhibition of ERCC1-XPF.

Elmenoufy AH, Gentile F, Jay D, Karimi-Busheri F, Yang X, Soueidan OM, Weilbeer C, Mani RS, Barakat KH, Tuszynski JA, Weinfeld M, West FG.

J Med Chem. 2019 Sep 12;62(17):7684-7696. doi: 10.1021/acs.jmedchem.9b00326. Epub 2019 Aug 22.

PMID:
31369707
3.

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

Ganesan A, Moon TC, Barakat KH.

Biochim Biophys Acta Gen Subj. 2018 Dec;1862(12):2764-2778. doi: 10.1016/j.bbagen.2018.08.010. Epub 2018 Aug 10.

PMID:
30251665
4.

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

Ganesan A, Arulraj T, Choulli T, Barakat KH.

BMC Med Inform Decis Mak. 2018 Jun 11;18(1):37. doi: 10.1186/s12911-018-0606-x.

6.

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

Jalily Hasani H, Ganesan A, Ahmed M, Barakat KH.

PLoS One. 2018 Feb 14;13(2):e0191905. doi: 10.1371/journal.pone.0191905. eCollection 2018.

7.

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

Kalyaanamoorthy S, Barakat KH.

Expert Opin Drug Discov. 2018 Mar;13(3):207-210. doi: 10.1080/17460441.2018.1418319. Epub 2017 Dec 18. No abstract available.

PMID:
29240515
8.

Development of Safe Drugs: The hERG Challenge.

Kalyaanamoorthy S, Barakat KH.

Med Res Rev. 2018 Mar;38(2):525-555. doi: 10.1002/med.21445. Epub 2017 May 3. Review.

PMID:
28467598
9.

Modelling DNA Repair Pathways: Recent Advances and Future Directions.

Gentile F, Tuszynski JA, Barakat KH.

Curr Pharm Des. 2016;22(23):3527-46. Review.

PMID:
27093954
10.

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

Gentile F, Tuszynski JA, Barakat KH.

J Mol Graph Model. 2016 Apr;65:71-82. doi: 10.1016/j.jmgm.2016.02.010. Epub 2016 Feb 26.

PMID:
26939044
11.

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

Kassem S, Ahmed M, El-Sheikh S, Barakat KH.

J Mol Graph Model. 2015 Nov;62:105-117. doi: 10.1016/j.jmgm.2015.09.010. Epub 2015 Sep 15. Review.

PMID:
26407139
12.

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

El-labbad EM, Ismail MA, Abou Ei Ella DA, Ahmed M, Wang F, Barakat KH, Abouzid KA.

Chem Biol Drug Des. 2015 Dec;86(6):1518-27. doi: 10.1111/cbdd.12621. Epub 2015 Aug 27.

PMID:
26212366
13.

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.

Anwar-Mohamed A, Barakat KH, Bhat R, Noskov SY, Tyrrell DL, Tuszynski JA, Houghton M.

Toxicol Lett. 2014 Nov 4;230(3):382-92. doi: 10.1016/j.toxlet.2014.08.007. Epub 2014 Aug 13.

PMID:
25127758
14.

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

Barakat KH, Anwar-Mohamed A, Tuszynski JA, Robins MJ, Tyrrell DL, Houghton M.

J Chem Inf Model. 2015 Feb 23;55(2):362-73. doi: 10.1021/ci400631n. Epub 2014 Apr 14.

PMID:
24730573
15.

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

Barakat KH, Law J, Prunotto A, Magee WC, Evans DH, Tyrrell DL, Tuszynski J, Houghton M.

J Chem Inf Model. 2013 Nov 25;53(11):3031-43. doi: 10.1021/ci4003969. Epub 2013 Oct 24.

PMID:
24116674
16.

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

Barakat KH, Huzil JT, Jordan KE, Evangelinos C, Houghton M, Tuszynski J.

Mol Pharm. 2013 Dec 2;10(12):4572-89. doi: 10.1021/mp4003893. Epub 2013 Nov 5.

PMID:
24094068
17.

Small molecule inhibitors of ERCC1-XPF protein-protein interaction synergize alkylating agents in cancer cells.

Jordheim LP, Barakat KH, Heinrich-Balard L, Matera EL, Cros-Perrial E, Bouledrak K, El Sabeh R, Perez-Pineiro R, Wishart DS, Cohen R, Tuszynski J, Dumontet C.

Mol Pharmacol. 2013 Jul;84(1):12-24. doi: 10.1124/mol.112.082347. Epub 2013 Apr 11.

PMID:
23580445
18.

Virtual screening and biological evaluation of inhibitors targeting the XPA-ERCC1 interaction.

Barakat KH, Jordheim LP, Perez-Pineiro R, Wishart D, Dumontet C, Tuszynski JA.

PLoS One. 2012;7(12):e51329. doi: 10.1371/journal.pone.0051329. Epub 2012 Dec 14.

19.

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

Craddock TJ, St George M, Freedman H, Barakat KH, Damaraju S, Hameroff S, Tuszynski JA.

PLoS One. 2012;7(6):e37251. doi: 10.1371/journal.pone.0037251. Epub 2012 Jun 25.

20.

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

Barakat KH, Gajewski MM, Tuszynski JA.

Drug Discov Today. 2012 Aug;17(15-16):913-20. doi: 10.1016/j.drudis.2012.04.008. Epub 2012 Apr 25. Review.

PMID:
22561893
21.

Discovery of small molecule inhibitors that interact with γ-tubulin.

Friesen DE, Barakat KH, Semenchenko V, Perez-Pineiro R, Fenske BW, Mane J, Wishart DS, Tuszynski JA.

Chem Biol Drug Des. 2012 May;79(5):639-52. doi: 10.1111/j.1747-0285.2012.01340.x. Epub 2012 Feb 15.

PMID:
22268380
22.

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

Barakat KH, Torin Huzil J, Luchko T, Jordheim L, Dumontet C, Tuszynski J.

J Mol Graph Model. 2009 Sep;28(2):113-30. doi: 10.1016/j.jmgm.2009.04.009. Epub 2009 May 4.

PMID:
19473860

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