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. Bhatt, R, Koes, DR, Durrant, JD. CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. J Chem Inf Model. 2024;64 (12):4651-4660. doi: 10.1021/acs.jcim.4c00825. PubMed PMID:38847393 PubMed Central PMC11200255.
  2. Agbavor, C, Zimnicka, A, Kumar, A, George, JL, Torres, M, Prehna, G et al.. The chaperone PrsA2 regulates the secretion, stability, and folding of listeriolysin O during Listeria monocytogenes infection. mBio. 2024;15 (7):e0074324. doi: 10.1128/mbio.00743-24. PubMed PMID:38809022 .
  3. Kochnev, Y, Ahmed, M, Maldonado, AM, Durrant, JD. MolModa: accessible and secure molecular docking in a web browser. Nucleic Acids Res. 2024;52 (W1):W498-W506. doi: 10.1093/nar/gkae406. PubMed PMID:38783339 PubMed Central PMC11223821.
  4. Barts, N, Bhatt, RH, Toner, C, Meyer, WK, Durrant, JD, Kohl, KD et al.. Functional convergence in gastric lysozymes of foregut-fermenting rodents, ruminants, and primates is not attributed to convergent molecular evolution. Comp Biochem Physiol B Biochem Mol Biol. 2024;271 :110949. doi: 10.1016/j.cbpb.2024.110949. PubMed PMID:38341948 .
  5. RECOVERY Collaborative Group. Immunomodulatory therapy in children with paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS, MIS-C; RECOVERY): a randomised, controlled, open-label, platform trial. Lancet Child Adolesc Health. 2024;8 (3):190-200. doi: 10.1016/S2352-4642(23)00316-4. PubMed PMID:38272046 .
  6. Ahmed, M, Maldonado, AM, Durrant, JD. From byte to bench to bedside: molecular dynamics simulations and drug discovery. BMC Biol. 2023;21 (1):299. doi: 10.1186/s12915-023-01791-z. PubMed PMID:38155355 PubMed Central PMC10755930.
  7. Ahmed, M, Maldonado, AM, Durrant, JD. From Byte to Bench to Bedside: Molecular Dynamics Simulations and Drug Discovery. ArXiv. 2023; :. . PubMed PMID:38076508 PubMed Central PMC10705576.
  8. Nguyen, NH, Sarangi, S, McChesney, EM, Sheng, S, Durrant, JD, Porter, AW et al.. Genome mining yields putative disease-associated ROMK variants with distinct defects. PLoS Genet. 2023;19 (11):e1011051. doi: 10.1371/journal.pgen.1011051. PubMed PMID:37956218 PubMed Central PMC10695394.
  9. Bhatt, R, Koes, DR, Durrant, JD. CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. bioRxiv. 2023; :. doi: 10.1101/2023.10.18.562959. PubMed PMID:37904961 PubMed Central PMC10614872.
  10. RECOVERY Collaborative Group. Empagliflozin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial. Lancet Diabetes Endocrinol. 2023;11 (12):905-914. doi: 10.1016/S2213-8587(23)00253-X. PubMed PMID:37865101 PubMed Central PMC10957483.
  11. Menchon, G, Maveyraud, L, Czaplicki, G. Molecular Dynamics as a Tool for Virtual Ligand Screening. Methods Mol Biol. 2024;2714 :33-83. doi: 10.1007/978-1-0716-3441-7_3. PubMed PMID:37676592 .
  12. Hellemann, E, Durrant, JD. Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling. J Chem Theory Comput. 2023;19 (17):5677-5689. doi: 10.1021/acs.jctc.3c00478. PubMed PMID:37585617 PubMed Central PMC10500992.
  13. Hellemann, E, Durrant, JD. Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling. bioRxiv. 2023; :. doi: 10.1101/2023.05.03.539330. PubMed PMID:37251500 PubMed Central PMC10214482.
  14. Lesko, MA, Chandrashekarappa, DG, Jordahl, EM, Oppenheimer, KG, Bowman, RW 2nd, Shang, C et al.. Changing course: Glucose starvation drives nuclear accumulation of Hexokinase 2 in S. cerevisiae. PLoS Genet. 2023;19 (5):e1010745. doi: 10.1371/journal.pgen.1010745. PubMed PMID:37196001 PubMed Central PMC10228819.
  15. Young, LA, Maughan, PJ, Jarvis, DE, Hunt, SP, Warner, HC, Durrant, KK et al.. A chromosome-scale reference of Chenopodium watsonii helps elucidate relationships within the North American A-genome Chenopodium species and with quinoa. Plant Genome. 2023;16 (3):e20349. doi: 10.1002/tpg2.20349. PubMed PMID:37195017 .
  16. van Wieren, A, Durrant, JD, Majumdar, S. Computational and experimental analyses of alanine racemase suggest new avenues for developing allosteric small-molecule antibiotics. Drug Dev Res. 2023;84 (5):999-1007. doi: 10.1002/ddr.22068. PubMed PMID:37129190 PubMed Central PMC10524904.
  17. RECOVERY Collaborative Group. Electronic address:, RECOVERY Collaborative Group. Higher dose corticosteroids in patients admitted to hospital with COVID-19 who are hypoxic but not requiring ventilatory support (RECOVERY): a randomised, controlled, open-label, platform trial. Lancet. 2023;401 (10387):1499-1507. doi: 10.1016/S0140-6736(23)00510-X. PubMed PMID:37060915 PubMed Central PMC10156147.
  18. Hellemann, E, Nallathambi, A, Durrant, JD. Allosteric inhibition of TEM-1 β lactamase: Microsecond molecular dynamics simulations provide mechanistic insights. Protein Sci. 2023;32 (4):e4622. doi: 10.1002/pro.4622. PubMed PMID:36906819 PubMed Central PMC10044111.
  19. Kochnev, Y, Durrant, JD. FPocketWeb: protein pocket hunting in a web browser. J Cheminform. 2022;14 (1):58. doi: 10.1186/s13321-022-00637-0. PubMed PMID:36008829 PubMed Central PMC9414105.
  20. Durrant, JD. Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization. J Comput Aided Mol Des. 2022;36 (9):677-686. doi: 10.1007/s10822-022-00471-4. PubMed PMID:36008698 PubMed Central PMC9512884.
  21. RECOVERY Collaborative Group. Baricitinib in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial and updated meta-analysis. Lancet. 2022;400 (10349):359-368. doi: 10.1016/S0140-6736(22)01109-6. PubMed PMID:35908569 PubMed Central PMC9333998.
  22. Wang, A, Durrant, JD. Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery. Molecules. 2022;27 (14):. doi: 10.3390/molecules27144623. PubMed PMID:35889494 PubMed Central PMC9319651.
  23. Tembo, M, Bainbridge, RE, Lara-Santos, C, Komondor, KM, Daskivich, GJ, Durrant, JD et al.. Phosphate position is key in mediating transmembrane ion channel TMEM16A-phosphatidylinositol 4,5-bisphosphate interaction. J Biol Chem. 2022;298 (8):102264. doi: 10.1016/j.jbc.2022.102264. PubMed PMID:35843309 PubMed Central PMC9396059.
  24. Hellemann, E, Walker, JL, Lesko, MA, Chandrashekarappa, DG, Schmidt, MC, O’Donnell, AF et al.. Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics. PLoS Comput Biol. 2022;18 (3):e1009929. doi: 10.1371/journal.pcbi.1009929. PubMed PMID:35235554 PubMed Central PMC8920189.
  25. Ottilie, S, Luth, MR, Hellemann, E, Goldgof, GM, Vigil, E, Kumar, P et al.. Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance. Commun Biol. 2022;5 (1):128. doi: 10.1038/s42003-022-03076-7. PubMed PMID:35149760 PubMed Central PMC8837787.
  26. Young, J, Garikipati, N, Durrant, JD. BINANA 2: Characterizing Receptor/Ligand Interactions in Python and JavaScript. J Chem Inf Model. 2022;62 (4):753-760. doi: 10.1021/acs.jcim.1c01461. PubMed PMID:35129332 PubMed Central PMC8889568.
  27. Green, H, Koes, DR, Durrant, JD. DeepFrag: a deep convolutional neural network for fragment-based lead optimization. Chem Sci. 2021;12 (23):8036-8047. doi: 10.1039/d1sc00163a. PubMed PMID:34194693 PubMed Central PMC8208308.
  28. Green, H, Durrant, JD. DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization. J Chem Inf Model. 2021;61 (6):2523-2529. doi: 10.1021/acs.jcim.1c00103. PubMed PMID:34029094 PubMed Central PMC8243318.
  29. Spiegel, JO, Van Houten, B, Durrant, JD. PARP1: Structural insights and pharmacological targets for inhibition. DNA Repair (Amst). 2021;103 :103125. doi: 10.1016/j.dnarep.2021.103125. PubMed PMID:33940558 PubMed Central PMC8206044.
  30. Spiegel, JO, Durrant, JD. AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. J Cheminform. 2020;12 (1):25. doi: 10.1186/s13321-020-00429-4. PubMed PMID:33431021 PubMed Central PMC7165399.
  31. Ha, EJ, Lwin, CT, Durrant, JD. LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates. J Cheminform. 2020;12 (1):69. doi: 10.1186/s13321-020-00471-2. PubMed PMID:33292486 PubMed Central PMC7656723.
  32. Ellison, MA, Walker, JL, Ropp, PJ, Durrant, JD, Arndt, KM. MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations. G3 (Bethesda). 2020;10 (9):3009-3014. doi: 10.1534/g3.120.401396. PubMed PMID:32605926 PubMed Central PMC7466961.
  33. Kochnev, Y, Hellemann, E, Cassidy, KC, Durrant, JD. Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser. Bioinformatics. 2020;36 (16):4513-4515. doi: 10.1093/bioinformatics/btaa579. PubMed PMID:32559277 PubMed Central PMC7575045.
  34. Cassidy, KC, Šefčík, J, Raghav, Y, Chang, A, Durrant, JD. ProteinVR: Web-based molecular visualization in virtual reality. PLoS Comput Biol. 2020;16 (3):e1007747. doi: 10.1371/journal.pcbi.1007747. PubMed PMID:32231351 PubMed Central PMC7147804.
  35. Durrant, JD, Kochanek, SE, Casalino, L, Ieong, PU, Dommer, AC, Amaro, RE et al.. Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ACS Cent Sci. 2020;6 (2):189-196. doi: 10.1021/acscentsci.9b01071. PubMed PMID:32123736 PubMed Central PMC7048371.
  36. Cassidy, KC, Lahr, RM, Kaminsky, JC, Mack, S, Fonseca, BD, Das, SR et al.. Capturing the Mechanism Underlying TOP mRNA Binding to LARP1. Structure. 2019;27 (12):1771-1781.e5. doi: 10.1016/j.str.2019.10.006. PubMed PMID:31676287 PubMed Central PMC7269035.
  37. Pacheco, S, Kaminsky, JC, Kochnev, IK, Durrant, JD. PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser. J Chem Inf Model. 2019;59 (10):4087-4092. doi: 10.1021/acs.jcim.9b00703. PubMed PMID:31580061 PubMed Central PMC6849643.
  38. Ropp, PJ, Spiegel, JO, Walker, JL, Green, H, Morales, GA, Milliken, KA et al.. Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. J Cheminform. 2019;11 (1):34. doi: 10.1186/s13321-019-0358-3. PubMed PMID:31127411 PubMed Central PMC6534830.
  39. Ropp, PJ, Kaminsky, JC, Yablonski, S, Durrant, JD. Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules. J Cheminform. 2019;11 (1):14. doi: 10.1186/s13321-019-0336-9. PubMed PMID:30767086 PubMed Central PMC6689865.
  40. Amaro, RE, Ieong, PU, Huber, G, Dommer, A, Steven, AC, Bush, RM et al.. A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target. ACS Cent Sci. 2018;4 (11):1570-1577. doi: 10.1021/acscentsci.8b00666. PubMed PMID:30555910 PubMed Central PMC6276040.
  41. 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.
  42. 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 .
  43. 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.
  44. 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 PubMed Central PMC6544362.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.
  52. 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.
  53. 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.
  54. 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.
  55. 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.
  56. 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.
  57. 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/ PubMed PMID:24667124 PubMed Central PMC4040315.
  58. 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.
  59. 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.
  60. 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.
  61. 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.
  62. 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.
  63. 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.
  64. 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.
  65. 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.
  66. 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.
  67. 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.
  68. 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.
  69. 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.
  70. 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.
  71. 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.
  72. 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.
  73. 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.
  74. 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.
  75. 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.
  76. 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.
  77. 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.
  78. 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.
  79. 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.
  80. 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.
  81. 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.
  82. Durrant, JD, de Oliveira, CA, McCammon, JA. Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. J Mol Recognit. 2010;23 (2):173-82. doi: 10.1002/jmr.989. PubMed PMID:19882751 PubMed Central PMC2950069.
  83. 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.
  84. 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.
  85. 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.
  86. Durrant, JD, Gardunia, BW, Livingstone, KD, Stevens, MR, Jellen, EN. An algorithm for analyzing linkages affected by heterozygous translocations: QuadMap. J Hered. 2006;97 (1):62-6. doi: 10.1093/jhered/esj002. PubMed PMID:16394257 .
  87. 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.
  88. 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.
  89. Durrant, JD, Amaro, RE. In De novo Molecular Design; Schneider, G., Ed.; Wiley-VCH: Weinheim, Germany, 2013.
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