Bibliography:

  1. Burkhalter, J..H., Olson, A.J., Hanson, J.C. and Nordman, C.E. (1968) Synthesis and x-ray structure of the 8,13-diaza-steroid system. Chem. Comm. 21:1274.

  2. Olson, A.J., Hanson, J.C., and Nordman, C.E. (1975) The crystal and molecular structure of () -2,3-dimethoxy-18-nor-8,13-diaza-1,3,5,(10)-estratrien-17-one. Acta Cryst. B31:496-501.

  3. Olson, A.J., Templeton, D.H. and Templeton, L.K. (1977) 6-endo-hydroxy-3-[2,2,1] heptane-2-endo-carboxylic acid lactam. Acta Cryst. B33:2266-2269.

  4. Harrison, S.C., Olson, A.J., Schutt, C.E., Winkler, F.K. and Bricogne, G. (1978) Tomato bushy stunt virus at 2.9 A resolution. Nature 276:368-373.

  5. Olson, A.J., editor, Computers in Crystallography Newsletter, Winter, 1979.

  6. O'Donnell, T.J. and Olson, A.J. (1981) GRAMPS - A graphics language interpreter for real-time interactive three-dimensional picture editing and animation. Computer Graphics 15:133-142.

  7. Olson, A.J., editor, Computer Simulation of Organic and Biological Molecules, Proceedings NRCC Workshop (1979) Lawrence Berkelely Laboratory Report 12979.

  8. Lester, W.A. Jr., DuPuis, M., O'Donnell, T.J., Olson, A.J. (1982) Some computational trends in theoretical chemistry. IUPAC Frontiers of Chemistry, K.J. Laidler, ed., Pergamon Press, New York.

  9. Olson, A.J. (1981) GRAMPS: A high level graphics interpreter for expanding graphics utilization. In Computing in Crystallography, Proceedings International Summer School in Crystallographic Computing, October, 1981.

  10. Lerner, R.A., Green, N., Olson, A.J., Shinnick, T. and Sutcliffe, J.G. (1981) The development of synthetic vaccines. Hospital Practice 16:55-62.

  11. Green, N., Alexander, H., Olson, A.J., Alexander, S., Shinnick, T.M., Sutcliffe, J.G. and Lerner, R.A. (1982) The immunogenic structure of the influenza virus hemagglutinin. Cell 28:477-487.

  12. Alden, R.A., Bricogne, G., Freer, S.T., Hall, S.R., Hendrickson, W.A., Machin, P.A., Munn, R.J., Olson, A.J., Reeke, G.N. Jr., Sherriff, S., Stewart, J.M., Sygusch, J., TenEyck, L.F. and Watenpaugh, K.D. (1983) Cooperative programming in crystallography. Computers and Chemistry 7(3):137-148.

  13. Olson, A.J., Bricogne, G., and Harrison, S.C. (1983) Structure of tomato bushy stunt virus IV; the virus particle at 2.9 A resolution. J. Mol. Biol. 171:61-93.

  14. Olson, A.J. (1983) Computer graphics in biomolecular science. Proc. Japan Computer Graphics Soc. December, 1983.

  15. Tainer, J.A., Getzoff, E.D., Alexander, H., Houghten, R.A.., Olson, A.J., Lerner, R.A. and Hendrickson, W.A. (1984) The reactivity of antipeptide antibodies is a function of the atomic mobility of sites in a protein. Nature 312:127-133.

  16. Tainer, J.A., Getzoff, E.D., Paterson, Y., Olson, A.J. and Lerner, R.A. (1985) The atomic mobility component of protein antigenicity. Ann. Rev. Immunol. 3:501-535.

  17. Connolly, M.L and Olson, A.J. (1985) GRANNY, a companion to GRAMPS for the real-time manipulation of macromolecular models. Computers and Chemistry 9:1-6.

  18. Tainer, J.A., Getzoff, E.D., Sayre, J. and Olson, A.J. (1985) Modeling intermolecular intractions: topography, mobility and electrostatic recognition. J. Mol. Graphics 3:103-105.

  19. Getzoff, E.D., Tainer, J.A. and Olson, A.J. (1986) Recognition and interactions controlling the assemblies of b barrel domains. Biophysics J. 49:191-206.

  20. Tainer, J.A., Getzoff, E.D. and Olson, A.J. (1986) Recognition and antigenicity. In Molecular Dynamics and Protein Structure, J. Hermans, ed., University of North Carolina, Chapel Hill, pp. 110-115.

  21. Getzoff, E.D., Olson, A.J., and Tainer, J.A. (1986) Anatomy of an enzyme: computer graphics views of Cu,Zn superoxide dismutase. In Superoixde and Superoxide Dismutase in Chemistry, Biology and Medicine, G. Rotilio, ed. Elsevier, Holland, pp. 135-140.

  22. Lai, E.H.C., Kabat, E.A., Meienhofer, J., Heimer, E.P., Olson, A..J., Lerner, R.A. (1987) Inhibition of phophorylcholine binding to antibodies using synthetic peptides. Nature 325:168-171.

  23. Olson, A.J., Tainer, J.A. and Getzoff, E.D. (1987) Computer graphics in the study of macromolecular interactions. In Crystallography in Molecular Biology, D. Moras, J. Drenth, B. Strandborg, D. Suck and K. Wilson, eds. Plenum, New York, pp. 131-139.

  24. Shea, R.G., Hopkings, P.B. and Olson, A.J. (1987) Probews for double helical DNA sequence information: molecular mechanics study of a proposed model. J. Biomolec. Struct. and Dynam. 5:313-326.

  25. Olson, A.J. (1987) Three-dimnesional computer presentation and animation of biological molecules. In Imaging and Visual Docmentation in Medicine, K. Wamsteker, U. Jonas, G. Van der Veen, P.F.G.M. Van Weis, eds. Proc. DOCUMED EUROPE `87, Elsevier.

  26. Goodsell, D.S., Mian, I.S. and Olson, A.J. 1989) Rendering of volumetric data in molecular systems. J Mol. Graphics 7:41-47.

  27. Goodsell, D.S. and Olson, A.J. (1989) Molecular applications of volume rendering and 3-D texture maps. In Proceedings of the Volume Visualization Workshop. Chapel Hill, NC.

  28. Goodsell, D.S. and Olson, A.J. (1990) Automated docking of substrates to proteins by simulated annealing. Proteins 8:195-202.

  29. Goodsell, D.S. and Olson, A.J. (1990) Rendering of volumetric data in biolgical systems. In Bioimaging and Two-Dimensional Spectroscopy, L.C. Smith, ed. Proc. SPIE 1205:117-124.

  30. Olson, A.J. and Goodsell, D.S. (1991) Visualization Blackboard: a functional view of proteins. IEEE Comp. Graphics and Appl. 11:15-17.

  31. Mian, I.S. Bradwell, A.R. and Olson, A.J. (1991) Structure, function and properties of antibody binding sites. J. Mol. Biol. 217:133-151.

  32. Olson, A.J. and Goodsell, D.S. (1992) Visualizing Biological Molecules. Sci. Am., 267(5):76-81.

  33. Roberts, V.A., Freeman, H.C., Olson, A.J., Tainer, J.A. and Getzoff, E.D. (1991) Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c. J. Biol. Chem. 266:13431-13441.

  34. Goodsell, D.S. and Olson, A.J. (1991) Molecular illustration. PIXEL 2:36-41.

  35. Goodsell, D.S. and Olson, A.J. (1992) Molecular illustration in black and white. J. Mol. Graphics, 10:235-240.

  36. Duncan, B.S. and Olson, A.J. (1992) Approximation and characterization of molecular surfaces. Biopolymers, 33:219-229.

  37. Duncan, B.S. and Olson, A.J. (1993) Shape analysis of molecular surfaces. Biopolymers, 33:231-238.

  38. Goodsell, D.S. and Olson, A.J. (1993) Macromolecular graphics. Current Opinion in Structural Biology, 2:193-201.

  39. Goodsell, D.S., Lauble, H., Stout, C.D. and Olson, A.J. (1993) Automated docking in crystallography: analysis of the substrates of aconitase. Proteins: Struct., Funct. & Genetics 17:1-10.

  40. Goodsell, D.S. and Olson, A.J. (1993) Soluble proteins: size, shape and function. TIBS 18(3):65-68.

  41. Olson, A.J. and Morris, G.M. (1993) Seeing our way to drug design. Perspectives in Drug Discovery amd Design 1:329-344.

  42. Duncan, B.S., Pique, M. and Olson, A.J. (1993) AVS for molecular modelling. Volume 3, Proccedings of the 2nd Annual International AVS User Group Conference, Lake Buena Vista, Florida, paper no. 93.

  43. Duncan, B.S. and Olson, A.J. (1994) AVStool: An interface to the AVS command line interpreter. Proceedings of the 3rd Annual International AVS User Group Conference, Boston, Massachusetts, pp. 128-141.

  44. Duncan, B.S. and Olson, A.J. (1995) Approximation and visualization of large-scale motion of protein surfaces. J. Mol. Graphics, in press.

  45. Duncan, B.S. and Olson, A.J. (1995) Texture mapping parametric molecular surfaces. J. Mol. Graphics, in press.

  46. Reva, B.A., Rykunov, D.S., Olson, A.J. and Finkelstein, A.V. (1995) Constructing lattice models of protein chains with side groups. J. Comp. Biol., in press.

  47. Sanner, M.F. and Olson, A.J. (1995) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, in press.

  48. Reva, B.A., Sanner, M.F., Olson, A.J. and Finkelstein, A.V. (1995) Lattice modeling: accuracy of energy calculations. Submitted, J. Comp. Chem.

  49. Sanner, M.F. and Olson, A.J., Spehner, J.C. (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, 38: 305-320.

  50. Reva, B.A., Sanner, M.F., Olson, A.J. and Finkelstein, A.V. (1996) Lattice modeling: accuracy of energy calculations. J. Comp. Chem. 17:1025-1032.

  51. Goodsell, D.S., Morris, G.M., Olson, A.J. Automated docking of flexible ligands: Applications of AutoDock. J. Mol. Recognit. 9:1, 1996.

  52. Reva, B.A., Finkelstein, A.V. Sanner, M.F., and Olson, A.J. (1996) Adjusting potential energy functions for lattice models of chain molecules. Proteins: Struct., Funct., Genetics, 25:379-388.

  53. Reva, B., Finkelstein, A.V., Rykunov, D.S. and Olson, A.J. (1996) Building Self Avoiding Lattice Models of Proteins Using an SCF-Optimization. Proteins: Struct., Funct., Genetics, 26:1-8.

  54. Strynadka, N.C.J., Eisenstein, M., Katchalski-Katzir, E., Shoichet, B.K., Kuntz, I.D., Abagyan, R., Totrov, M., Janin, J., Cherfils, J., F. Zimmerman, Olson, A., Duncan, B., Rao, M., Jackson, R., Sternberg, M. and James, M.N.G. (1996) Molecular docking programs successfully predict the binding of a (-lactamase inhibitory protein to TEM-1 (-lactamase. Nature Struct. Biol. 3:233-239.

  55. Morris, G.M., Goodsell, D.S., Huey, R., Olson, A.J. (1996) Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. J. Computer-Aided Mol. Design, 10:293-304.

  56. Sanner, M.F., Olson, A.J. (1997) Real time surface reconstruction for moving molecular fragments. In Pacific Symposium on Biocomputing '97, R. B. Altman, A.K. Dunker, L. Hunter, T.E. Klein, eds. World Scientific Press, Singapore, pp. 385-396.

  57. Reva, B.A., Finkelstein, A.V., Sanner, M.F., Olson, A.J. (1997) Accurate mean-force pairwise residue potentials for discrimination of protein folds. In Pacific Symposium on Biocomputing '97, R. B. Altman, A.K. Dunker, L. Hunter, T.E. Klein, eds. World Scientific Press, Singapore, pp. 373-384.

  58. Reva, B.A., Finkelstein, A.V., Sanner, M.F., Olson, A.J. (1997) Residue-residue mean-force potentials for protein structure recognition. Prot. Eng. 10:865-876.

  59. Olson, A.J. and Pique, M.E. (1998) Visualizing the Future of Molecular Graphics. Proc. SAR QSAR Environ. Res., 8:273-285.

  60. Olson, A.J. and Goodsell, D.S. (1998) Automated docking and the search for HIV protease inhibitors. Proc. SAR QSAR Environ. Res., 8:233-247.

  61. Laco, G.S., Schalk-Hihi, C., Lubkowski, J., Zdanov, A., Morris, G.M., Olson, A.J., Elder, J.H., Wlodawer, A., Gustchina, A. (1997) Crystal structures of the inactive D30N mutant of FIV protease complexed with a substrate and an inhibitor. Biochemistry 36:10696-10708.

  62. Laco, G.S., Fitzgerald, M., Morris, G.M., Olson, A.J., Kent, S.B.H., Elder, J.H. (1997) Molecular analysis of the FIV protease; generation of a novel form of the protease by autoproteolysis and construction of cleavage resistant proteases. J. Virology 71:5505-5511.

  63. Reva, B.A., Finkelstein, A.V., Sanner, M., Olson, A.J., Skolnick, J. (1997) Recognition of protein structure on coarse lattices with residue-residue energy functions. Prot. Eng. 10:1123-1130.

  64. Larsen, T.A., Olson, A.J., Goodsell, D.S. (1998) Morphology of protein-protein interfaces. Structure, 6:421-427.

  65. Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K., Olson, A.J. (1998) Automated docking using Lamarckian genetic algorithm and an empirical binding free energy function. J. Comp. Chem. 19(14):1639-1662.

  66. Rosin, C.D., Belew, R.K., Morris, G.M., Olson, A.J. & Goodsell, D.S. (1998) Computational Coevolution of Antiviral Drug Resistance. Artificial Life4, 41-59.

  67. Sanner, M.F., Duncan, B.S., Carrillo, C.J., Olson, A.J. (1999) Integrating computation and visualization for biomolecular analysis: an example using PYTHON and AVS. In: BIOCOMPUTING '99 Proceedings of the Pacific Symposium Mauna Lani, Hawaii, USA 4 - 9 January 1999, R. B. Altman, K. Lauderdale, A. K. Dunker , L. Hunter , T.E.Klein , eds. World Scientific Press.

  68. Rao, M.S. and Olson, A.J. (1999) Modelling of Factor Xa-inhibitor complexes: a computational flexible docking approach. Proteins: Struct., Function and Genetics 34(2):173-183.

  69. Ruf, W., Shobe, J., Rao, S.M., Dickinson, C.D., Olson, A.J., Edgington, T.S. (1999) Importance of Factor VIIa Gla-domain residue Arg-36 for recognition of the macromolecular substrate Factor X Gla-domain. Biochemistry, 38(7)1957-1966.

  70. Lee, T., Le, V.-D., Lim, D., Lin, Y.-C., Morris, G.M., Wong, A.L., Olson, A.J., Elder, J.H., Wong, C.-H. (1999) Development of a new type of protease inhibitors, efficacious against FIV and HIV variants. J. Am. Chem. Soc. 121:1145-1155.

  71. Rosin, C.D., Belew, R.K., Morris, G.M., Olson, A.J. (1999) Coevolutionary analysis of resistance-evading peptidomimetic inhibitors of HIV-1 protease. Proc. Natl. Acad. Sci. USA 96:1369-1374.

  72. Soares, T.A., Goodsell, D.S., Briggs, J.M., Ferreira, R., Olson, A.J. (1999) Docking of 4-oxalocrotonate tautomerase substrates: implications for the catalytic mechanism. In press, Biopolymers.

  73. Rosin, C., Belew, R., Walker, W., Morris, G., Olson, A., Goodsell, D.S. (1999) Coevolution and subsite decomposition for the design of resistance-evading HIV1 protease inhibitors. J. Mol. Biol. 287(1):77-92.

  74. Macke, T.J., Duncan, B.S., Goodsell, D.S. & Olson, A.J. (1999) Interactive Modeling of Supramolecular Assemblies. J. Mol. Graphics and Modelling 16:115-120.

  75. Goodsell, D.S. and Olson, A.J. (1999) Structural symmetry and protein function. Annual Review of Biophysics and Biomolecular Structure, vol. 29, in press.

  76. Coombs, G.S., Rao, M.S., Olson, A.J., Dawson, P.E., Madison, E.L. (1999) Revisiting catalysis by chymotrypsin family serine proteases using peptide substrates and inhibitors with unnatural main chains J. Biol. Chem. 274: 24074-24079.

  77. Olson, A.J. (2000) Molecular graphics and animation. In International Tables for Crystallography, Vol. F. M. Rossmann and E. Arnold, eds. In press.

  78. Morris, G.M., Olson, A.J. and Goodsell, D.S. (2000) Protein ligand docking. In: Evolutionary Algorithms in Molecular Design, D.E. Clark, ed. Wiley VCH, in press.

  79. Soares, T., Goodsell, D.S., Ferreira, R., Olson, A.J., Briggs, J.M. (2000) Ionization State and Molecular Docking Studies for the Macrophage Inhibitory Factor: the Role of Lysine 32 in the Catalytic Mechanism. J. Molec. Recognition 13, 146-156.

  80. Zhao, S., Goodsell, D.S., Olson, A. J. (2001) Analysis of a dataset of paired uncomplexed protein structures: new metrics for sidechain flexibility and model evaluation.  Proteins: Struct., Func. & Genetics, 43:271-279.

  81. Coon, S.I., Sanner, M.F., Olson, A.J. (2001) Re-usable components for structural bioinformatics. Proc. Ninth International Python Conference, March 5-8, 2001, Long Beach, CA. 10 pgs.

  82. Nunn, R., Macke, T.J., Olson, A.J., Yeager, M. (2001) Transmembrane-helices in the gap junction membrane channel: systematic search of packing models based on the pair potential function.Microscopy Res. Tech. 52:344-351.

  83. Zhang, Y.-M., Rao, M.S., Heath, R.J., Price, A.C., Olson, A.J., Rock, C.O., White, S.W. (2001) Identification and analysis of the acyl carrier protein (ACP) docking site on beta-ketoacyl-ACP synthase III. J. Biol. Chem. 276:8231-8238.

  84. Osterberg, F., Morris, G.M., Sanner, M.F., Olson, A.J., Goodsell, D.S. (2001) Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins: Struct., Function, Genetics 46:34-40

  85. Beuhler, B., Lin, Y.-C., Morris, G., Olson, A.J., Wong, C.-H., Richman, D.D., Elder, J.H., Torbett, B.E. (2001) Viral evolution in response to the broad-based retroviral protease inhibitor TL-3.  J. Virology 75:9502-9508.

  86. Zhao, S., Morris, G.M., Olson, A.J., Goodsell, D.S. (2001) Recognition templates for predicting adenylate and guanylate binding sites in proteins.  J. Mol. Biol. 314:1249-1258.

  87. Sanner, M.F., Stoffler, D., Olson, A.J. (2002) ViPEr, a visual programming environment for Python. Proc. 10th International Python Conference, February 4-7, 2002, Alexandria, VA, 15 pgs. ISBN 1-930792-05-0.

  88. Stoffler, D., Sanner, M., Morris, G.M., Olson, A.J., Goodsell, D. (2002) Evolutionary analysis of HIV-1 protease inhibitors: methods for design of inhibitors that evade resistance.Proteins, Structure, Function & Genetics 48:63-74.

  89. Legge, G.B., Morris, G.M., Sanner, M.F., Takada, Y., Olson, A.J., Grynszpan, F. (2002) Model of the 2 integrin I-domain/ICAM-1 DI interface suggests that subtle changes in loop orientation determine ligand specificity. Proteins: Structure, Funct., Genetics 48:151-160.

  90. Rosenfeld, R.J., Garcin, E.D., Panda, K., Andersson, G., Anders, A., Wallace, A.V., Morris, G.M., Olson, A.J., Stuehr, D.J., Tainer, J.A., Getzoff, E.D. (2002) Conformational changes in nitric oxide synthases induced by chlorzoxazone and nitroindazoles: crystallographic and computational analyses of inhibitor potency. Biochemistry 41(47); 13915-13925.

  91. Stoffler, D., Coon, S.I., Huey, R., Olson, A.J., Sanner, M.F. (2003) Integrating biomolecular analysis and visual programming: flexibility and interactivity in the design of bioinformatics tools. Proc. 36th Annual Hawaii International Conference on Systems Sciences (CD/ROM), Jan. 6-9, 2003, Computer Society Press, 10 pages

  92. Norledge, B.V., Petrovan, R.J., Ruf, W., Olson, A.J.(2003) The tissue factor/factor VIIa/factor Xa complex: a model built by docking and site-directed mutagenesis.Proteins: Struct., Funct. Genetics 53:640-648.

  93. Mak, C.C., Brik, A., Lerner, D.L., Elder, J.H., Morris, G.M., Olson, A.J., Wong, C.-H. (2003) Design and synthesis of broad-based mono- and bi- cyclic inhibitors of FIV and HIV proteases. Bioorg. Med. Chem. 11:2025-2040.

  94. Lin, Y.-C., Beck, Z., Morris, G.M., Olson, A.J., Elder, J.H. (2003) Structural basis for distinctions between substrate and inhibitor specificities for feline immunodeficiency virus and human immunodeficiency virus proteases. J. Virology, 77:6589-6600.

  95. Huang, H., Norledge, B.V., Liu, C., Olson, A.J., Edgington, T.S. (2003) Selective attenuation of the extrinsic limb of the tissue factor-driven coagulation protease cascade by occupancy of a novel peptidyl docking site on tissue factor. Biochemistry, 42:10619-10626.

  96. Rosenfeld, R.J., Goodsell, D.S., Musah, R.A., Morris, G.M., Goodin, D.B., Olson, A.J. (2003) Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. J. Computer-Aided Mol. Design 17:525-536.

  97. Zhang, Y., Desharnais, J., Marsilje, T.H., Li, C., Hedrick, P., Gooljarsingh, L.T., Tavassoli, A., Benkovic, S.J., Olson, A.J., Boger, D.L., Wilson, I.A. (2003) Rational design, synthesis, evaluation and crystal structure of a potent inhibitor of human GAR Tfase: 10-trifluoracetyl-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid.Biochemistry 42:6043-6056.

  98. Brik, A., Muldoon, J., Lin, Y.-C., Elder, J.H., Goodsell, D.S., Olson, A.J., Fokin, V.V., Sharpless, K.B., Wong, C.-H. (2003) Rapid diversity-oriented synthesis in microtiter plates for in situ screening of HIV protease inhibitors. ChemBioChem 4:1246-1248.

  99. Huey, R., Goodsell, D.S., Morris, G.M., Olson, A.J. (2004) Grid-based hydrogen bond potentials with improved directionality. Lett. Drug Des. & Disc. 1:178-183.

  100. Zhu, X., Tanaka, F., Hu, Y., Heine, A., Fuller, R., Zhong, G., Olson, A.J., Lerner, R.A., Barbas, C.F., Wilson, I.A. (2004) The origin of enantioselectivity in aldolase antibodies: crystal structure, site-directed mutagenesis, and computational analysis. J. Mol. Biol. 343:1269-1280.

  101. Li, C., Xu, L., Wolan, D., Wilson, I.A., Olson, A.J. (2004) Virtual Screening of Human AICAR Transformylase against the NCI Diversity set using AutoDock to Identify Novel Non-Folate Inhibitors. J. Med. Chem. 47(27) : 6681-6690.

  102. Sankaranarayana, G., Weghorst, S., Sanner, M.F., Gillet, A., Olson, A.J. (2003) Role of Haptics in Teaching structural Molecular Biology <. In Proc. of 11th international Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems, March 22-23 2003 Los Angels Ca. IEEE committee on Visualization and Graphics. pp. 363-266. ISBN 0-7695-1890-7.

  103. Gillet, A., Goodsell, D., Sanner, M.F., Stoffler, D., Weghorst, S. Winn, W., Olson, A.J. (2004) Computer-Linked Autofabricated 3D Model For Teaching Structural Biology.In Proc. SIGGRAPH 2004.

  104. Gillet, A., Goodsell, D., Sanner, M., Stoffler, D., Olson, A.J. (2004) A Tangible Model Augmented Reality Application for Molecular Biology. in Proceeding of IEEE Visualization 2004, p235-241.

  105. Gillet, A., Sanner, M., Stoffler, D., Olson, A.J. (2005) Tangible interfaces for structural molecular biology. Structure:13:483-491.

  106. Brik, A., Alexandratos, J., Lin, Y.-C., Elder, J.H., Olson, A.J., Goodsell, D.S., Wong, C.-H. (2005) 1,2,3-Triazole as a peptider surrogate in the rapid synthesis of HIV-1 protease inhibitors. ChemBioChem 6:1167-1169.

  107. Dickerson, T.J., Beuscher, A., Rogers, C.J., Hixon, M.S., Yamamoto, N., Xu, Y., Olson, A.J., Janda, K.D. (2005) Discovery of Acetylcholinesterase peripheral anionic site ligands through computational refinement of a directed library. Biochemistry 44:14845-14853.

  108. Beuscher, A., Olson, A.J., Goodsell, D.S. (2005) Identifying protein binding sites and optimal ligands.Lett. Drug Des. & Disc. 2:255-259.

  109. Varjragupta, O., Boonchong, P., Morris, G.M., Olson, A.J. (2005) Active site binding modes of curcumin in HIV-1 protease and integrase. Bioorg. & Med. Chem. Lett., 15:3364-3368.

  110. Rogers, J.P., Beuscher,A..E. III,Flajolet, M., McAvoy,T., Nairn, A.C., Olson, A.J., Greengard, P. (2006) Discovery of protein phosphatase 2C inhibitors by virtual screening. J. Med. Chem.49:1658-1667

  111. Jiang, Z., Georgel, P., Li, C., Choe, J., Crozat, K., Rutschmann, S., Du, X., Bigby, T., Mudd, S., Sovath, S., Wilson, I.A., Olson, A.J., Beutler, B. (2006) Details of a Toll-like receptor by germline mutagenesis. PNAS 103:10961-10966.

  112. Eubanks, L.M., Rogers, C.J., Beuscher, A.E. IV, Koob, G.F., Olson, A.J., Dickerson, T.J., Janda, K.D. (2006) A molecular link between the active component of marijuana and Alzheimer's disease pathology. Mol. Pharm, 10.1021/mp060066m

  113. Harris, R., Olson, A.J., Goodsell, D.S. Automated prediction of ligand-binding sites in proteins. Proteins 70:1506, 2007

  114. Huey, R., Morris, G.M., Olson, A.J., Goodsell, D.S. (2007) A semi-empirical free energy force field with charge-based desolvation. J. Comp. Chem. 28(6): 1145-1152.

  115. Chang, M., Lindstrom, W., Olson, A.J., Belew, R.K. (2007) Analysis of wild-type and mutant structures via in silico docking against diverse ligand libraries. J. Chem. Information & Modeling 47(3):1258-1262.

  116. Amaro, R., Minh, D.L., Cheng, L., Lindstrom, W.M. Jr., Olson, Arthur J., Lin, J.-H., Li, W., McCammon, A. (2007) Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J. Am. Chem. Soc. 129(25):7764-7765.

  117. Beuscher, A.E. IV and Olson, A.J. (2007) Iterative docking strategies for virtual ligand screening. In Computational and Structural Approaches to Drug Discovery, R.M. Stroud and J. Finer-Moore, eds. RSC Publishing, London, pp. 242-264.

  118. Olson, A.J. and Keinan, E. (2007) Chemical mimicry of viral capsid self-assembly. PNAS, 104(52):20731-20736.

  119. Evans, M.J., Morris, G.M., Wu, J., Olson, A.J., Sorenson, E.J., Cravatt, B.F. (2007) Mechanistic and structural requirements for active site labeling of phosphoglycerate mutase by spiroepoxides. Mol. Biosyst. 3:496.

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