Publications

Dr. Durrant and the members of his lab have published a number of peer-reviewed scientific articles describing computer-aided drug-discovery methods and applications.

Cover art designed by Jacob Durrant.
Cover art designed by Jacob Durrant.

  1. Ottilie, S, Goldgof, GM, Cheung, AL, Walker, JL, Vigil, E, Allen, KE et al.. Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies. J Cheminform. 2018;10 (1):6. doi: 10.1186/s13321-018-0261-3. PubMed PMID:29464421 PubMed Central PMC5820243.
  2. Rajendiran, N, Durrant, JD. Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques. J Comput Chem. 2018;39 (12):748-755. doi: 10.1002/jcc.25155. PubMed PMID:29280166 .
  3. Ropp, P, Friedman, A, Durrant, JD. Scoria: a Python module for manipulating 3D molecular data. J Cheminform. 2017;9 (1):52. doi: 10.1186/s13321-017-0237-8. PubMed PMID:29086076 PubMed Central PMC5603467.
  4. Abraham, MM, Denton, RE, Harper, RW, Scott, WL, O’Donnell, MJ, Durrant, JD et al.. Documenting and harnessing the biological potential of molecules in Distributed Drug Discovery (D3) virtual catalogs. Chem Biol Drug Des. 2017;90 (5):909-918. doi: 10.1111/cbdd.13012. PubMed PMID:28453915 .
  5. Ottilie, S, Goldgof, GM, Calvet, CM, Jennings, GK, LaMonte, G, Schenken, J et al.. Rapid Chagas Disease Drug Target Discovery Using Directed Evolution in Drug-Sensitive Yeast. ACS Chem. Biol. 2017;12 (2):422-434. doi: 10.1021/acschembio.6b01037. PubMed PMID:27977118 PubMed Central PMC5649375.
  6. Goldgof, GM, Durrant, JD, Ottilie, S, Vigil, E, Allen, KE, Gunawan, F et al.. Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor. Sci Rep. 2016;6 :27806. doi: 10.1038/srep27806. PubMed PMID:27291296 PubMed Central PMC4904242.
  7. Durrant, JD, Bush, RM, Amaro, RE. Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants. J Phys Chem B. 2016;120 (33):8590-9. doi: 10.1021/acs.jpcb.6b02655. PubMed PMID:27141956 PubMed Central PMC5002936.
  8. Wagner, JR, Lee, CT, Durrant, JD, Malmstrom, RD, Feher, VA, Amaro, RE et al.. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem. Rev. 2016;116 (11):6370-90. doi: 10.1021/acs.chemrev.5b00631. PubMed PMID:27074285 PubMed Central PMC4901368.
  9. Durrant, JD, Carlson, KE, Martin, TA, Offutt, TL, Mayne, CG, Katzenellenbogen, JA et al.. Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands. J Chem Inf Model. 2015;55 (9):1953-61. doi: 10.1021/acs.jcim.5b00241. PubMed PMID:26286148 PubMed Central PMC4780411.
  10. Ikram, NK, Durrant, JD, Muchtaridi, M, Zalaludin, AS, Purwitasari, N, Mohamed, N et al.. A virtual screening approach for identifying plants with anti H5N1 neuraminidase activity. J Chem Inf Model. 2015;55 (2):308-16. doi: 10.1021/ci500405g. PubMed PMID:25555059 PubMed Central PMC4340357.
  11. Durrant, JD, Amaro, RE. Machine-learning techniques applied to antibacterial drug discovery. Chem Biol Drug Des. 2015;85 (1):14-21. doi: 10.1111/cbdd.12423. PubMed PMID:25521642 PubMed Central PMC4273861.
  12. Durrant, JD, Votapka, L, Sørensen, J, Amaro, RE. POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. J Chem Theory Comput. 2014;10 (11):5047-5056. doi: 10.1021/ct500381c. PubMed PMID:25400521 PubMed Central PMC4230373.
  13. Tallorin, LC, Durrant, JD, Nguyen, QG, McCammon, JA, Burkart, MD. Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase. Bioorg. Med. Chem. 2014;22 (21):6053-6061. doi: 10.1016/j.bmc.2014.09.002. PubMed PMID:25284249 PubMed Central PMC4807855.
  14. Durrant, JD, Amaro, RE. LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PLoS Comput. Biol. 2014;10 (7):e1003720. doi: 10.1371/journal.pcbi.1003720. PubMed PMID:25032790 PubMed Central PMC4102414.
  15. Durrant, JD, Amaro, RE. WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. BMC Bioinformatics. 2014;15 :159. doi: 10.1186/1471-2105-15-159. PubMed PMID:24886360 PubMed Central PMC4094277.
  16. Van Wart, AT, Durrant, J, Votapka, L, Amaro, RE. Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis. J Chem Theory Comput. 2014;10 (2):511-517. doi: 10.1021/ct4008603. PubMed PMID:24803851 PubMed Central PMC3958135.
  17. Feher, VA, Durrant, JD, Van Wart, AT, Amaro, RE. Computational approaches to mapping allosteric pathways. Curr. Opin. Struct. Biol. 2014;25 :98-103. doi: 10.1016/j.sbi.2014.02.004. PubMed PMID:24667124 PubMed Central PMC4040315.
  18. Durrant, JD, Lindert, S, McCammon, JA. AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. J. Mol. Graph. Model. 2013;44 :104-12. doi: 10.1016/j.jmgm.2013.05.006. PubMed PMID:23792207 PubMed Central PMC3842281.
  19. Durrant, JD, Friedman, AJ, Rogers, KE, McCammon, JA. Comparing neural-network scoring functions and the state of the art: applications to common library screening. J Chem Inf Model. 2013;53 (7):1726-35. doi: 10.1021/ci400042y. PubMed PMID:23734946 PubMed Central PMC3735370.
  20. Rogers, KE, Keränen, H, Durrant, JD, Ratnam, J, Doak, A, Arkin, MR et al.. Novel cruzain inhibitors for the treatment of Chagas’ disease. Chem Biol Drug Des. 2012;80 (3):398-405. doi: 10.1111/j.1747-0285.2012.01416.x. PubMed PMID:22613098 PubMed Central PMC3503458.
  21. Lindert, S, Durrant, JD, McCammon, JA. LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders. Chem Biol Drug Des. 2012;80 (3):358-65. doi: 10.1111/j.1747-0285.2012.01414.x. PubMed PMID:22594624 PubMed Central PMC3462068.
  22. Friedman, AJ, Durrant, JD, Pierce, LC, McCorvie, TJ, Timson, DJ, McCammon, JA et al.. The molecular dynamics of Trypanosoma brucei UDP-galactose 4′-epimerase: a drug target for African sleeping sickness. Chem Biol Drug Des. 2012;80 (2):173-81. doi: 10.1111/j.1747-0285.2012.01392.x. PubMed PMID:22487100 PubMed Central PMC3399956.
  23. Durrant, JD, McCammon, JA. AutoClickChem: click chemistry in silico. PLoS Comput. Biol. 2012;8 (3):e1002397. doi: 10.1371/journal.pcbi.1002397. PubMed PMID:22438795 PubMed Central PMC3305364.
  24. Durrant, JD, McCammon, JA. Molecular dynamics simulations and drug discovery. BMC Biol. 2011;9 :71. doi: 10.1186/1741-7007-9-71. PubMed PMID:22035460 PubMed Central PMC3203851.
  25. Durrant, JD, McCammon, JA. NNScore 2.0: a neural-network receptor-ligand scoring function. J Chem Inf Model. 2011;51 (11):2897-903. doi: 10.1021/ci2003889. PubMed PMID:22017367 PubMed Central PMC3225089.
  26. Durrant, JD, Friedman, AJ, McCammon, JA. CrystalDock: a novel approach to fragment-based drug design. J Chem Inf Model. 2011;51 (10):2573-80. doi: 10.1021/ci200357y. PubMed PMID:21910501 PubMed Central PMC3206965.
  27. Durrant, JD, McCammon, JA. HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. J. Mol. Graph. Model. 2011;31 :5-9. doi: 10.1016/j.jmgm.2011.07.008. PubMed PMID:21880522 PubMed Central PMC3218086.
  28. Durrant, JD, McCammon, JA. Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors. BMC Pharmacol. 2011;11 :9. doi: 10.1186/1471-2210-11-9. PubMed PMID:21878090 PubMed Central PMC3196686.
  29. Durrant, JD, Cao, R, Gorfe, AA, Zhu, W, Li, J, Sankovsky, A et al.. Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. Chem Biol Drug Des. 2011;78 (3):323-32. doi: 10.1111/j.1747-0285.2011.01164.x. PubMed PMID:21696546 PubMed Central PMC3155669.
  30. Durrant, JD, de Oliveira, CA, McCammon, JA. Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitors. Chem Biol Drug Des. 2011;78 (2):191-8. doi: 10.1111/j.1747-0285.2011.01148.x. PubMed PMID:21609408 PubMed Central PMC3135671.
  31. Durrant, JD, McCammon, JA. BINANA: a novel algorithm for ligand-binding characterization. J. Mol. Graph. Model. 2011;29 (6):888-93. doi: 10.1016/j.jmgm.2011.01.004. PubMed PMID:21310640 PubMed Central PMC3099006.
  32. Sinko, W, de Oliveira, C, Williams, S, Van Wynsberghe, A, Durrant, JD, Cao, R et al.. Applying molecular dynamics simulations to identify rarely sampled ligand-bound conformational states of undecaprenyl pyrophosphate synthase, an antibacterial target. Chem Biol Drug Des. 2011;77 (6):412-20. doi: 10.1111/j.1747-0285.2011.01101.x. PubMed PMID:21294851 PubMed Central PMC3095679.
  33. Durrant, JD, de Oliveira, CA, McCammon, JA. POVME: an algorithm for measuring binding-pocket volumes. J. Mol. Graph. Model. 2011;29 (5):773-6. doi: 10.1016/j.jmgm.2010.10.007. PubMed PMID:21147010 PubMed Central PMC3063076.
  34. Durrant, JD, McCammon, JA. Computer-aided drug-discovery techniques that account for receptor flexibility. Curr Opin Pharmacol. 2010;10 (6):770-4. doi: 10.1016/j.coph.2010.09.001. PubMed PMID:20888294 PubMed Central PMC3026641.
  35. Durrant, JD, McCammon, JA. NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes. J Chem Inf Model. 2010;50 (10):1865-71. doi: 10.1021/ci100244v. PubMed PMID:20845954 PubMed Central PMC2964041.
  36. Durrant, JD, Hall, L, Swift, RV, Landon, M, Schnaufer, A, Amaro, RE et al.. Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1. PLoS Negl Trop Dis. 2010;4 (8):e803. doi: 10.1371/journal.pntd.0000803. PubMed PMID:20808768 PubMed Central PMC2927429.
  37. Durrant, JD, Urbaniak, MD, Ferguson, MA, McCammon, JA. Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4′-epimerase inhibitors: toward the development of novel therapies for African sleeping sickness. J. Med. Chem. 2010;53 (13):5025-32. doi: 10.1021/jm100456a. PubMed PMID:20527952 PubMed Central PMC2895357.
  38. Durrant, JD, Keränen, H, Wilson, BA, McCammon, JA. Computational identification of uncharacterized cruzain binding sites. PLoS Negl Trop Dis. 2010;4 (5):e676. doi: 10.1371/journal.pntd.0000676. PubMed PMID:20485483 PubMed Central PMC2867933.
  39. Durrant, JD, McCammon, JA. Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. Comput Biol Chem. 2010;34 (2):97-105. doi: 10.1016/j.compbiolchem.2010.03.005. PubMed PMID:20427241 PubMed Central PMC2896249.
  40. Durrant, JD, Amaro, RE, Xie, L, Urbaniak, MD, Ferguson, MA, Haapalainen, A et al.. A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput. Biol. 2010;6 (1):e1000648. doi: 10.1371/journal.pcbi.1000648. PubMed PMID:20098496 PubMed Central PMC2799658.
  41. Mustafa, M, Busath, DD. The gramicidin channel ion permeation free-energy profile: direct and indirect effects of CHARMM force field improvements. Interdiscip Sci. 2009;1 (2):113-27. doi: 10.1007/s12539-009-0025-3. PubMed PMID:20084184 PubMed Central PMC2806686.
  42. Durrant, JD, de Oliveira, CA, McCammon, JA. Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. J. Mol. Recognit. ;23 (2):173-82. doi: 10.1002/jmr.989. PubMed PMID:19882751 PubMed Central PMC2950069.
  43. Durrant, JD, Amaro, RE, McCammon, JA. AutoGrow: a novel algorithm for protein inhibitor design. Chem Biol Drug Des. 2009;73 (2):168-78. doi: 10.1111/j.1747-0285.2008.00761.x. PubMed PMID:19207419 PubMed Central PMC2724963.
  44. Swift, RV, Durrant, J, Amaro, RE, McCammon, JA. Toward understanding the conformational dynamics of RNA ligation. Biochemistry. 2009;48 (4):709-19. doi: 10.1021/bi8018114. PubMed PMID:19133737 PubMed Central PMC2651658.
  45. Durrant, JD, Caywood, D, Busath, DD. Tryptophan contributions to the empirical free-energy profile in gramicidin A/M heterodimer channels. Biophys. J. 2006;91 (9):3230-41. doi: 10.1529/biophysj.105.078782. PubMed PMID:16861266 PubMed Central PMC1614506.
  46. Durrant, JD, Gardunia, BW, Livingstone, KD, Stevens, MR, Jellen, EN. An algorithm for analyzing linkages affected by heterozygous translocations: QuadMap. J. Hered. ;97 (1):62-6. doi: 10.1093/jhered/esj002. PubMed PMID:16394257 .
  47. Scott, WL, Denton, RE, Marrs, KA, Durrant, JD, Samaritoni, JG, Abraham, MM, et al. Distributed Drug Discovery: Advancing Chemical Education through Contextualized Combinatorial Solid-Phase Organic Laboratories. J Chem Educ. 2015;92 (5):819.
  48. Singharoy, A, Chandler, D, Durrant, JD, Sener, M, Amaro, R, Schulten, K. The Do’s and Do Not’s of a 100 Million Atom Molecular Dynamics Simulation. Biophys J. 2015;108(2):158a.
  49. Durrant, JD, Amaro, RE. In De novo Molecular Design; Schneider, G., Ed.; Wiley-VCH: Weinheim, Germany, 2013.
  50. Duffin, RL, Garrett, MP, Thompson, KB, Durrant, JD, Busath, DD. Modulation of lipid bilayer interfacial dipole potential by phloretin, RH421, and 6-ketocholestanol as probed by gramicidin channel conductanceLangmuir 2003;19(4):1439.
  51. Jellen, EN, Gardunia, BW, Durrant, JD, Raymond, FD, Murphy, JP, Livingston, DP, Santos, AG. In American Oat Workers Conference Proceedings 2002.

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