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Items: 1 to 20 of 51

1.

Capturing the Mechanism Underlying TOP mRNA Binding to LARP1.

Cassidy KC, Lahr RM, Kaminsky JC, Mack S, Fonseca BD, Das SR, Berman AJ, Durrant JD.

Structure. 2019 Oct 29. pii: S0969-2126(19)30347-8. doi: 10.1016/j.str.2019.10.006. [Epub ahead of print]

PMID:
31676287
2.

PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser.

Pacheco S, Kaminsky JC, Kochnev IK, Durrant JD.

J Chem Inf Model. 2019 Oct 28;59(10):4087-4092. doi: 10.1021/acs.jcim.9b00703. Epub 2019 Oct 16.

PMID:
31580061
3.

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening.

Ropp PJ, Spiegel JO, Walker JL, Green H, Morales GA, Milliken KA, Ringe JJ, Durrant JD.

J Cheminform. 2019 May 24;11(1):34. doi: 10.1186/s13321-019-0358-3.

4.

Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules.

Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD.

J Cheminform. 2019 Feb 14;11(1):14. doi: 10.1186/s13321-019-0336-9.

5.

A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target.

Amaro RE, Ieong PU, Huber G, Dommer A, Steven AC, Bush RM, Durrant JD, Votapka LW.

ACS Cent Sci. 2018 Nov 28;4(11):1570-1577. doi: 10.1021/acscentsci.8b00666. Epub 2018 Nov 9.

6.

Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies.

Ottilie S, Goldgof GM, Cheung AL, Walker JL, Vigil E, Allen KE, Antonova-Koch Y, Slayman CW, Suzuki Y, Durrant JD.

J Cheminform. 2018 Feb 20;10(1):6. doi: 10.1186/s13321-018-0261-3.

7.

Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques.

Rajendiran N, Durrant JD.

J Comput Chem. 2018 May 5;39(12):748-755. doi: 10.1002/jcc.25155. Epub 2017 Dec 26.

PMID:
29280166
8.

Scoria: a Python module for manipulating 3D molecular data.

Ropp P, Friedman A, Durrant JD.

J Cheminform. 2017 Sep 18;9(1):52. doi: 10.1186/s13321-017-0237-8.

9.

Documenting and harnessing the biological potential of molecules in Distributed Drug Discovery (D3) virtual catalogs.

Abraham MM, Denton RE, Harper RW, Scott WL, O'Donnell MJ, Durrant JD.

Chem Biol Drug Des. 2017 Nov;90(5):909-918. doi: 10.1111/cbdd.13012. Epub 2017 Jun 12.

10.

Rapid Chagas Disease Drug Target Discovery Using Directed Evolution in Drug-Sensitive Yeast.

Ottilie S, Goldgof GM, Calvet CM, Jennings GK, LaMonte G, Schenken J, Vigil E, Kumar P, McCall LI, Lopes ES, Gunawan F, Yang J, Suzuki Y, Siqueira-Neto JL, McKerrow JH, Amaro RE, Podust LM, Durrant JD, Winzeler EA.

ACS Chem Biol. 2017 Feb 17;12(2):422-434. doi: 10.1021/acschembio.6b01037. Epub 2016 Dec 23.

11.

Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor.

Goldgof GM, Durrant JD, Ottilie S, Vigil E, Allen KE, Gunawan F, Kostylev M, Henderson KA, Yang J, Schenken J, LaMonte GM, Manary MJ, Murao A, Nachon M, Stanhope R, Prescott M, McNamara CW, Slayman CW, Amaro RE, Suzuki Y, Winzeler EA.

Sci Rep. 2016 Jun 13;6:27806. doi: 10.1038/srep27806.

12.

Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants.

Durrant JD, Bush RM, Amaro RE.

J Phys Chem B. 2016 Aug 25;120(33):8590-9. doi: 10.1021/acs.jpcb.6b02655. Epub 2016 May 12.

13.

Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.

Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE.

Chem Rev. 2016 Jun 8;116(11):6370-90. doi: 10.1021/acs.chemrev.5b00631. Epub 2016 Apr 13. Review.

14.

Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands.

Durrant JD, Carlson KE, Martin TA, Offutt TL, Mayne CG, Katzenellenbogen JA, Amaro RE.

J Chem Inf Model. 2015 Sep 28;55(9):1953-61. doi: 10.1021/acs.jcim.5b00241. Epub 2015 Sep 4.

15.

A virtual screening approach for identifying plants with anti H5N1 neuraminidase activity.

Ikram NK, Durrant JD, Muchtaridi M, Zalaludin AS, Purwitasari N, Mohamed N, Rahim AS, Lam CK, Normi YM, Rahman NA, Amaro RE, Wahab HA.

J Chem Inf Model. 2015 Feb 23;55(2):308-16. doi: 10.1021/ci500405g. Epub 2015 Jan 29.

16.

Machine-learning techniques applied to antibacterial drug discovery.

Durrant JD, Amaro RE.

Chem Biol Drug Des. 2015 Jan;85(1):14-21. doi: 10.1111/cbdd.12423.

17.

POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics.

Durrant JD, Votapka L, Sørensen J, Amaro RE.

J Chem Theory Comput. 2014 Nov 11;10(11):5047-5056. Epub 2014 Sep 29.

18.

Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase.

Tallorin LC, Durrant JD, Nguyen QG, McCammon JA, Burkart MD.

Bioorg Med Chem. 2014 Nov 1;22(21):6053-6061. doi: 10.1016/j.bmc.2014.09.002. Epub 2014 Sep 15.

19.

LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry.

Durrant JD, Amaro RE.

PLoS Comput Biol. 2014 Jul 17;10(7):e1003720. doi: 10.1371/journal.pcbi.1003720. eCollection 2014 Jul.

20.

WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets.

Durrant JD, Amaro RE.

BMC Bioinformatics. 2014 May 23;15:159. doi: 10.1186/1471-2105-15-159.

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