Publications

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  1. Singharoy, A.; Chandler, D.; Durrant, J. D.; Sener, M.; Amaro, R. E.; Schulten, K., The Do’s and Do Not’s of a 100 Million Atom Molecular Dynamics Simulation. Chemical Biology & Drug Design 2015, 108(2), 158a.
  2. Durrant, J. D.; Amaro, R. E., Machine‐Learning Techniques Applied to Antibacterial Drug Discovery. Chemical Biology & Drug Design 2015, 85(1), 14-21.
  3. Ikram, N. K. K.; Durrant, J. D.; Muchtaridi, M.; Zalaludin, A. S.; Purwitasari, N.; Mohamed, N.; Rahim, A. S. A.; Chan, K. L.; Normi, Y. M.; Rahman, N. A.; Amaro, R. E.; Wahab, H., A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity. Journal of Chemical Information and Modeling 2015, 55(2), 308-316.
  4. Durrant, J. D.; Amaro, R. E., Machine-Learning Techniques Applied to Antibacterial Drug Discovery. Chemical Biology & Drug Design 2015. 85(1), 14-21.
  5. Tallorin, L.; Durrant, J. D.; Nguyen, Q. G.; McCammon, J. A.; Burkart, M. D., Celastrol Inhibits Plasmodium falciparum Enoyl-Acyl Carrier Protein Reductase. Bioorganic & Medicinal Chemistry 2014, 22(21), 6053-6061. Shared first authorship.
  6. Durrant, J. D.; Votapka, L. A.; Sørensen, J.; Amaro, R. E., POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. Journal of Chemical Theory and Computation 2014. 10(11), 5047–5056.
  7. Feher, V. A.; Durrant, J. D.; Van Wart, A. T.; Amaro, R. E., Computational approaches to mapping allosteric pathways. Current Opinion in Structural Biology 2014, 25, 98-103. Cover article.
  8. Van Wart, A. T.; Durrant, J. D.; Votapka, L.; Amaro, R. E., Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis. Journal of Chemical Theory and Computation 2014, 10(2), 511-517. Shared first authorship.
  9. Durrant, J. D.; Amaro, R. E., WebChem Viewer: A Tool for the Easy Dissemination of Molecular-Structure and Chemical-Property Data. BMC Bioinformatics, 2014, 15(159).
  10. Durrant, J. D.; Amaro, R. E., LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry. PLoS Computational Biology 2014, 10(7), e1003720.
  11. Durrant, J. D.; Friedman, A. J.; Rogers, K. E.; McCammon, J. A., Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening. Journal of Chemical Information and Modeling 2013, 53(7), 1726-35.
  12. Durrant, J. D.; Lindert, S.; McCammon, J. A., AutoGrow 3.0: An Improved Algorithm for Chemically Tractable, Semi-Automated Protein Inhibitor Design. Journal of Molecular Graphics and Modelling 2013, 44, 104-112.
  13. Durrant, J. D.; McCammon, J. A., De Novo Design by Fragment Growing and Docking. In De novo Molecular Design, Schneider, G., Ed. Wiley-VCH: Weinheim, Germany, 2013; p 480.
  14. Rogers, K. E.; Keränen, H.; Durrant, J. D.; Ratnam, J.; Doak, A.; Arkin, M. R.; McCammon, J. A., Novel Cruzain Inhibitors for the Treatment of Chagas’ Disease. Chemical Biology & Drug Design 2012, 80(3), 398-405.
  15. Friedman, A. J.; Durrant, J. D.; Pierce, L. C. T.; McCorvie, T. J.; Timson, D. J.; McCammon, J. A, The Molecular Dynamics of Trypanosoma brucei UDP-Galactose 4′-Epimerase: A Drug Target for African Sleeping Sickness. Chemical Biology & Drug Design 2012, 80(2), 173-181.
  16. Lindert, S.; Durrant, J. D.; McCammon, J. A., LigMerge: A Fast Algorithm to Generate Models of Novel Potential Ligands from Sets of Known Binders. Chemical Biology & Drug Design 2012.
  17. Durrant, J. D.; McCammon, J. A., AutoClickChem: Click Chemistry in Silico. PLoS Computational Biology 2012, 8(3), e1002397.
  18. Durrant, J. D.; McCammon, J. A., Molecular dynamics simulations and drug discovery. BMC Biology 2011, 9, 71. “Highly accessed” article. Article recommended by the Faculty of 1000.
  19. Durrant, J. D.; Friedman, A. J.; McCammon, J. A., CrystalDock: a novel approach to fragment-based drug design. Journal of Chemical Information and Modeling 2011, 51(10), 2573-80.
  20. Durrant, J. D.; McCammon, J. A., NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function. Journal of Chemical Information and Modeling 2011, 51(11), 2897-2903.
  21. Durrant, J. D.; McCammon, J. A., Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors. BMC Pharmacology 2011, 11, 9.
  22. Durrant, J. D.; McCammon, J. A., HBonanza: A Computer Algorithm for Molecular-Dynamics-Trajectory Hydrogen-Bond Analysis. Journal of Molecular Graphics and Modelling 2011, 31, 5-9.
  23. Durrant, J. D.; Cao, R.; Gorfe, A. A.; Zhu, W.; Li, J.; Sankovsky, A.; Oldfield, E.; McCammon, J. A., Non-Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer-Aided Drug Design. Chemical Biology & Drug Design 2011, 78(3), 323-332. Shared first authorship. Cover article.
  24. Durrant, J. D.; Oliveira, C. d.; McCammon, J. A., Pyrone-Based Inhibitors of Metalloproteinases Types 2 and 3 May Work as Conformation-Selective Inhibitors. Computational Biology & Drug Design 2011, 78(2), 191-198. Cover article.
  25. Durrant, J. D.; McCammon, J. A., BINANA: A novel algorithm for ligand-binding characterization. Journal of Molecular Graphics and Modelling 2011, 29(6), 888-93.
  26. Durrant, J. D.; de Oliveira, C. A.; McCammon, J. A., POVME: An algorithm for measuring binding-pocket volumes. Journal of Molecular Graphics and Modelling 2011, 29(5), 773-6.
  27. Sinko, W.; de Oliveira, C.; Williams, S.; Van Wynsberghe, A.; Durrant, J. D.; Cao, R.; Oldfield, E.; McCammon, J. A., Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target. Chemical Biology & Drug Design 2011, 77(6), 412-420. Article recommended by the Faculty of 1000.
  28. Durrant, J. D.; McCammon, J. A., Computer-aided drug-discovery techniques that account for receptor flexibility. Current Opinion in Pharmacology 2010, 10(6), 770-774.
  29. More cover art

    More cover art

    Durrant, J. D.; McCammon, J. A., NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes. Journal of Chemical Information and Modeling 2010, 50(10), 1865-1871.

  30. Durrant, J. D.; Hall, L.; Swift, R. V.; Landon, M.; Schnaufer, A.; Amaro, R. E., Novel Naphthalene-Based Inhibitors of Trypanosoma brucei RNA Editing Ligase 1. PLoS Neglected Tropical Diseases 2010, 4(8), e803.
  31. Durrant, J. D.; Urbaniak, M. D.; Ferguson, M. A.; McCammon, J. A., Computer-Aided Identification of Trypanosoma brucei Uridine Diphosphate Galactose 4′-Epimerase Inhibitors: Toward the Development of Novel Therapies for African Sleeping Sickness. Journal of Medicinal Chemistry 2010, 53(13), 5025-5032.
  32. Durrant, J. D.; McCammon, J. A., Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. Computational Biology and Chemistry 2010, 34(2), 97-105.
  33. Durrant, J. D.; Keranen, H.; Wilson, B. A.; McCammon, J. A., Computational identification of uncharacterized cruzain binding sites. PLoS Neglected Tropical Diseases 2010, 4(5), e676. Shared first authorship.
  34. Durrant, J. D.; Amaro, R. E.; Xie, L.; Urbaniak, M. D.; Ferguson, M. A.; Haapalainen, A.; Chen, Z.; Di Guilmi, A. M.; Wunder, F.; Bourne, P. E.; McCammon, J. A., A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Computational Biology 2010, 6(1), e1000648.
  35. Durrant, J. D.; de Oliveira, C. A. F.; McCammon, J. A., Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. Journal of Molecular Recognition 2010, 23(2), 173-182.
  36. Swift, R. V.; Durrant, J. D.; Amaro, R. E.; McCammon, J. A., Toward understanding the conformational dynamics of RNA ligation. Biochemistry 2009, 48(4), 709-19. Shared first authorship.
  37. Durrant, J. D.; Amaro, R. E.; McCammon, J. A., AutoGrow: A Novel Algorithm for Protein Inhibitor Design. Chemical Biology & Drug Design 2009, 73(2), 168-178.
  38. Durrant, J. D.; Caywood, D.; Busath, D. D., Tryptophan contributions to the empirical free-energy profile in gramicidin A/M heterodimer channels. Biophysical Journal 2006, 91(9), 3230-41.
  39. Durrant, J. D.; Gardunia, B. W.; Livingstone, K. D.; Stevens, M. R.; Jellen, E. N., An algorithm for analyzing linkages affected by heterozygous translocations: QuadMap. Journal of Heredity 2006, 97(1), 62-6.
  40. Duffin, R. L.; Garrett, M. P.; Flake, K. B.; Durrant, J. D.; Busath, D. D., Modulation of lipid bilayer interfacial dipole potential by phloretin, RH421, and 6-ketocholestanol as probed by gramicidin channel conductance. Langmuir 2003, 19(8), 3561-3561.
  41. Jellen, E. N.; Gardunia, B. W.; Durrant, J. D.; Raymond, F. D.; Murphy, J. P.; Livingston, D. P.; Santos, A. G. In Segregation Patterns in Oat Populations Derived From Parents Heterozygous for Translocations 7C-17 and 6C-21. American Oat Workers Conference Proceedings, 2002.

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