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Molecular Docking

  • Protocol
Molecular Modeling of Proteins

Part of the book series: Methods Molecular Biology™ ((MIMB,volume 443))

Summary

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand—protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter discusses the background and theory of molecular docking software, and covers the usage of some of the most-cited docking software.

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References

  1. 1. Hendlich, M. (1998) Databases for protein-ligand complexes. Acta Crystallogr D Biol Crystallogr, 54(Pt 6 Pt 1): 1178–1182.

    Article  CAS  PubMed  Google Scholar 

  2. 2. Hu, L., Benson, M.L., Smith, R.D., Lerner, M.G., and Carlson, H.A. (2005) Binding MOAD (Mother Of All Databases). Proteins, 60(3): 333–340.

    Article  CAS  PubMed  Google Scholar 

  3. 3. Irwin, J.J. and Shoichet, B.K. (2005) ZINC—a free database of commercially available compounds for virtual screening. J Chem Inf Model, 45(1): 177–182.

    Article  CAS  PubMed  Google Scholar 

  4. 4. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Res, 28(1): 235–242.

    Article  CAS  PubMed  Google Scholar 

  5. 5. Pozzan, A. (2006) Molecular descriptors and methods for ligand based virtual high throughput screening in drug discovery. Curr Pharm Des, 12(17): 2099–2110.

    Article  CAS  PubMed  Google Scholar 

  6. 6. Hawkins, P.C., Skillman, A.G., and Nicholls, A. (2007) Comparison of shape-matching and docking as virtual screening tools. J Med Chem, 50(1): 74–82.

    Article  CAS  PubMed  Google Scholar 

  7. 7. Sousa, S.F., Fernandes, P.A., and Ramos, M.J. (2006) Protein-ligand docking: Current status and future challenges. Proteins, 65(1): 15–26.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  9. 9. Morris, G.M., Goodsell, D.S., Huey, R., and Olson, A.J. (1996) Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J Comput Aided Mol Des, 10(4): 293–304.

    Article  CAS  PubMed  Google Scholar 

  10. 10. Goodsell, D.S. and Olson, A.J. (1990) Automated docking of substrates to proteins by simulated annealing. Proteins, 8(3): 195–202.

    Article  CAS  PubMed  Google Scholar 

  11. 11. Ewing, T.J.A. and Kuntz, I.D. (1997) Critical evaluation of search algorithms for automated molecular docking and database screening. J Comput Chem, 18(9): 1175–1189.

    Article  CAS  Google Scholar 

  12. 12. Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., and Ferrin, T.E. (1982) A geometric approach to macromolecule-ligand interactions. J Mol Biol, 161(2): 269–288.

    Article  CAS  PubMed  Google Scholar 

  13. 13. Rarey, M., Kramer, B., Lengauer, T., and Klebe, G. (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol, 261(3): 470–489.

    Article  CAS  PubMed  Google Scholar 

  14. 14. Jones, G., Willett, P., Glen, R.C., Leach, A.R., and Taylor, R. (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol, 267(3): 727–748.

    Article  CAS  PubMed  Google Scholar 

  15. 15. Jones, G., Willett, P., and Glen, R.C. (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol, 245(1): 43–53.

    Article  CAS  PubMed  Google Scholar 

  16. 16. Abagyan, R.A., Totrov, M.M., and Kuznetzov, D.A. (1994) ICM—a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. Journal of Computational Chemistry, 15: 488–506.

    Article  CAS  Google Scholar 

  17. 17. Taylor, R.D., Jewsbury, P.J., and Essex, J.W. (2002) A review of protein-small molecule docking methods. J Comput Aided Mol Des, 16(3): 151–166.

    Article  CAS  PubMed  Google Scholar 

  18. 18. Bissantz, C., Folkers, G., and Rognan, D. (2000) Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem, 43(25): 4759–4767.

    Article  CAS  PubMed  Google Scholar 

  19. 19. Friesner, R.A., Banks, J.L., Murphy, R.B., Halgren, T.A., Klicic, J.J., Mainz, D.T., Repasky, M.P., Knoll, E.H., Shelley, M., Perry, J.K., Shaw, D.E., Francis, P., and Shenkin, P.S. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem, 47(7): 1739–1749.

    Article  CAS  PubMed  Google Scholar 

  20. 20. Halgren, T.A., Murphy, R.B., Friesner, R.A., Beard, H.S., Frye, L.L., Pollard, W.T., and Banks, J.L. (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem, 47(7): 1750–1759.

    Article  CAS  PubMed  Google Scholar 

  21. 21. Kellenberger, E., Rodrigo, J., Muller, P., and Rognan, D. (2004) Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins, 57(2): 225–242.

    Article  Google Scholar 

  22. 22. Kontoyianni, M., McClellan, L.M., and Sokol, G.S. (2004) Evaluation of docking performance: comparative data on docking algorithms. J Med Chem, 47(3): 558–565.

    Article  CAS  PubMed  Google Scholar 

  23. 23. Perola, E., Walters, W.P., and Charifson, P.S. (2004) A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins, 56(2): 235–249.

    Article  Google Scholar 

  24. 24. Evans, D.A. and Neidle, S. (2006) Virtual screening of DNA minor groove binders. J Med Chem, 49(14): 4232–4238.

    Article  CAS  PubMed  Google Scholar 

  25. 25. Evers, A., Hessler, G., Matter, H., and Klabunde, T. (2005) Virtual screening of biogenic amine-binding G-protein coupled receptors: comparative evaluation of protein- and ligand-based virtual screening protocols. J Med Chem, 48(17): 5448–5465.

    Article  CAS  PubMed  Google Scholar 

  26. 26. Cummings, M.D., DesJarlais, R.L., Gibbs, A.C., Mohan, V., and Jaeger, E.P. (2005) Comparison of automated docking programs as virtual screening tools. J Med Chem, 48(4): 962–976.

    Article  CAS  PubMed  Google Scholar 

  27. 27. Cotesta, S., Giordanetto, F., Trosset, J.Y., Crivori, P., Kroemer, R.T., Stouten, P.F., and Vulpetti, A. (2005) Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models. Proteins, 60(4): 629–643.

    Article  CAS  PubMed  Google Scholar 

  28. 28. Cole, J.C., Murray, C.W., Nissink, J.W., Taylor, R.D., and Taylor, R. (2005) Comparing protein-ligand docking programs is difficult. Proteins, 60(3): 325–332.

    Article  CAS  PubMed  Google Scholar 

  29. 29. Vigers, G.P. and Rizzi, J.P. (2004) Multiple active site corrections for docking and virtual screening. J Med Chem, 47(1): 80–89.

    Article  CAS  PubMed  Google Scholar 

  30. 30. Solis, F.J. and Wets, R.J.-B. (1981) Minimization by random search techniques. Mathematical Operations Research, 6: 19–30.

    Article  Google Scholar 

  31. 31. Conn, A.R., Gould, N.I.M., and Toint, P.L. (1991) A globally convergent augmented Lagrangian pattern search algorithm for optimization with general constraints and simple bounds. SIAM Journal on Numerical Analysis, 28(2): 545–572.

    Article  Google Scholar 

  32. 32. Kirkpatrick, S., C. D. Gelatt, J., and Vecchi, M.P. (1983) Optimization by simulated annealing. Science, 220(4598): 671–680.

    Article  CAS  PubMed  Google Scholar 

  33. 33. Holland, J.H., Adaptation in natural and artificial systems. 1992, Cambridge, MA: The MIT Press. 211.

    Google Scholar 

  34. 34. Goldberg, D.E., Genetic Algorithms in Search, Optimization and Machine Learning. 1st ed. 1989, Boston, MA: Addison-Wesley Longman Publishing Co., Inc. 372.

    Google Scholar 

  35. 35. Michalewicz, Z., Genetic Algorithms + Data Structures = Evolution Program. 3rd ed. 1996, London, UK: Springer-Verlag. 387.

    Google Scholar 

  36. 36. de Graaf, C., Oostenbrink, C., Keizers, P.H., van der Wijst, T., Jongejan, A., and Vermeulen, N.P. (2006) Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking. J Med Chem, 49(8): 2417– 2430.

    Article  PubMed  Google Scholar 

  37. 37. Diller, D.J. and Li, R. (2003) Kinases, homology models, and high throughput docking. J Med Chem, 46(22): 4638–4647.

    Article  CAS  PubMed  Google Scholar 

  38. 38. Evers, A. and Klabunde, T. (2005) Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor. J Med Chem, 48(4): 1088–1097.

    Article  CAS  PubMed  Google Scholar 

  39. 39. Shoichet, B.K., McGovern, S.L., Wei, B., and Irwin, J.J. (2002) Lead discovery using molecular docking. Curr Opin Chem Biol, 6(4): 439–446.

    Article  CAS  PubMed  Google Scholar 

  40. 40. Murray, C.W., Baxter, C.A., and Frenkel, A.D. (1999) The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. J Comput Aided Mol Des, 13(6): 547–562.

    Article  CAS  PubMed  Google Scholar 

  41. 41. Gunasekaran, K. and Nussinov, R. (2007) How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding. J Mol Biol, 365(1): 257–273.

    Article  CAS  PubMed  Google Scholar 

  42. 42. Alonso, H., Bliznyuk, A.A., and Gready, J.E. (2006) Combining docking and molecular dynamic simulations in drug design. Med Res Rev, 26(5): 531–568.

    Article  CAS  PubMed  Google Scholar 

  43. 43. Lin, J.H., Perryman, A.L., Schames, J.R., and McCammon, J.A. (2002) Computational drug design accommodating receptor flexibility: The relaxed complex scheme. J Am Chem Soc, 124(20): 5632–5633.

    Article  CAS  PubMed  Google Scholar 

  44. 44. Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, T.E., III, Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., Vincent, J.J., Crowley, M., Ferguson, D.M., Radmer, R.J., Seibel, G.L., Singh, U.C., Weiner, P.K., and Kollman, P.A. (1997) AMBER 5 University of California: San Francisco.

    Google Scholar 

  45. 45. Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, T.E., III, J., W., Ross, W.S., C., S., Darden, T., Merz, K.M., Stanton, R.V., Cheng, A., Vincent, J.J., Crowley, M., V., T., Gohlke, R.R., Duan, Y., Pitera, J., Massova, I., Seibel, G.L., Singh, C., Weiner, P., and Kollman, P.A. (2002) AMBER 7 University of California: San Francisco.

    Google Scholar 

  46. 46. Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., and Schulten, K. (2005) Scalable molecular dynamics with NAMD. J Comput Chem, 26: 1781–1802.

    Article  CAS  PubMed  Google Scholar 

  47. 47. Schames, J.R., Henchman, R.H., Siegel, J.S., Sotriffer, C.A., Ni, H., and McCammon, J.A. (2004) Discovery of a novel binding trench in HIV integrase. J Med Chem, 47(8): 1879–1881.

    Article  CAS  PubMed  Google Scholar 

  48. Gastreich, M., Lilienthal, M., Briem, H., and Claussen, H. (2006) Ultrafast de novo docking: combining pharmacophores and combinatorics. J Comput Aided Mol Des, in press.

    Google Scholar 

  49. 49. Gasteiger, J. and Marsili, M. (1978) A new model for calculating atomic charges in molecules. Tetrahedron Lett., 34: 3181–3184.

    Article  Google Scholar 

  50. 50. Mulakala, C., Nerinckx, W., and Reilly, P.J. (2006) Docking studies on glycoside hydrolase Family 47 endoplasmic reticulum alpha-(1 → 2)-mannosidase I to elucidate the pathway to the substrate transition state. Carbohydrate Research, 341(13): 2233–2245.

    Article  CAS  PubMed  Google Scholar 

  51. 51. Laederach, A. and Reilly, P.J. (2005) Modeling protein recognition of carbohydrates. Proteins-Structure Function and Bioinformatics, 60(4): 591–597.

    Article  CAS  Google Scholar 

  52. 52. Rockey, W.M., Laederach, A., and Reilly, P.J. (2000) Automated docking of alpha-(1 → 4)-and alpha-(1 → 6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site. Proteins-Structure Function and Genetics, 40(2): 299–309.

    Article  CAS  Google Scholar 

  53. 53. Rarey, M., Kramer, B., and Lengauer, T. (1995) Time-efficient docking of flexible ligands into active sites of proteins. Proc Int Conf Intell Syst Mol Biol, 3: 300–308.

    CAS  PubMed  Google Scholar 

  54. Gasteiger, J. and Sadowski, J. (1992) CORINA 3.4, Molecular Networks GmbH: Erlangen, Germany, http://www.molecular-networks.com/onlinedemos/corinademo.html.

  55. 55. Gasteiger, J., Rudolph, C., and Sadowski, J. (1992) Automatic generation of 3D-atomic coordinates for organic molecules. Tetrahedron Comput. Methodol., 3: 537–547.

    Article  Google Scholar 

  56. Pearlman, R.S. and Balducci, R. Confort: A Novel Algorithm For Conformational Analysis. in National Meeting of the American Chemical Society. 1998. New Orleans, LA.

    Google Scholar 

  57. Ten Eyck, L.F., Mandell, J., Roberts, V.A., and Pique, M.E., Surveying Molecular Interactions With DOT. 1995.

    Google Scholar 

  58. 58. Vakser, I.A. (1997) Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins, Suppl 1: 226–230.

    Article  CAS  PubMed  Google Scholar 

  59. 59. Tovchigrechko, A. and Vakser, I.A. (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Res, 34(Web Server issue): W310–314.

    Article  CAS  PubMed  Google Scholar 

  60. 60. Chen, R. and Weng, Z. (2002) Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins, 47(3): 281–294.

    Article  CAS  PubMed  Google Scholar 

  61. 61. Mohan, V., Gibbs, A.C., Cummings, M.D., Jaeger, E.P., and DesJarlais, R.L. (2005) Docking: successes and challenges. Curr Pharm Des, 11(3): 323–333.

    Article  CAS  PubMed  Google Scholar 

  62. 62. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, J., Kenneth M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., and Kollman, P.A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 117: 5179–5197.

    Article  CAS  Google Scholar 

  63. 63. Huey, R., Morris, G.M., Olson, A.J., and Goodsell, D.S. (2007) A semiempirical free energy force field with charge-based desolvation. J Comput Chem, 28(6): 1145–1152.

    Article  CAS  PubMed  Google Scholar 

  64. 64. Böhm, H.-J. (1994) The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des, 8(3): 243–256.

    Article  PubMed  Google Scholar 

  65. 65. Rosenfeld, R.J., Goodsell, D.S., Musah, R.A., Morris, G.M., Goodin, D.B., and Olson, A.J. (2003) Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. Journal of Computer-Aided Molecular Design, 17(8): 525–536.

    Article  CAS  PubMed  Google Scholar 

  66. 66. Ruvinsky, A.M. and Kozintsev, A.V. (2005) New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy. Journal of Computational Chemistry, 26(11): 1089–1095.

    Article  CAS  PubMed  Google Scholar 

  67. 67. Ruvinsky, A.M. and Kozintsev, A.V. (2006) Novel statistical-thermodynamic methods to predict protein-ligand binding positions using probability distribution functions. Proteins-Structure Function and Bioinformatics, 62(1): 202–208.

    Article  CAS  Google Scholar 

  68. 68. Cramer, C.J. and Truhlar, D.G. (1992) AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution. J Comput Aided Mol Des, 6(6): 629–666.

    Article  CAS  PubMed  Google Scholar 

  69. Hawkins, G.D., Giesen, D.J., Lynch, G.C., Chambers, C.C., Rossi, I., Storer, J.W., Li, J., Zhu, T., Thompson, J.D., Winget, P., Lynch, B.J., Rinaldi, D., Liotard, D.A., Cramer, C.J., and Truhlar, D.G. (2007) AMSOL 7.1, Department of Chemistry and Supercomputer Institute, University of Minnesota: Minneapolis, Minnesota, http://comp.chem.umn.edu/amsol/.

  70. 70. Vaque, M., Arola, A., Aliagas, C., and Pujadas, G. (2006) BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock. Bioinformatics, 22(14): 1803–1804.

    Article  CAS  PubMed  Google Scholar 

  71. 71. Smith, R.D., Hu, L., Falkner, J.A., Benson, M.L., Nerothin, J.P., and Carlson, H.A. (2006) Exploring protein-ligand recognition with Binding MOAD. J Mol Graph Model, 24(6): 414–425.

    Article  CAS  PubMed  Google Scholar 

  72. 72. Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18(15): 2714–2723.

    Article  CAS  PubMed  Google Scholar 

  73. 73. Davis, I.W., Murray, L.W., Richardson, J.S., and Richardson, D.C. (2004) MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res, 32(Web Server issue): W615–619.

    Article  CAS  PubMed  Google Scholar 

  74. 74. Lovell, S.C., Davis, I.W., Arendall, W.B., 3rd, de Bakker, P.I., Word, J.M., Prisant, M.G., Richardson, J.S., and Richardson, D.C. (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins, 50(3): 437–450.

    Article  CAS  PubMed  Google Scholar 

  75. Weininger, D., Daylight Theory Manual. 2006, Daylight Chemical Information Systems, Inc.

    Google Scholar 

  76. 76. Dalby, A., Nourse, J.G., Hounshell, W.D., Gushurst, A.K.I., Grier, D.L., Leland, B.A., and Laufer, J. (1992) Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited. J Chem Inf Comput Sci, 32: 244–255.

    CAS  Google Scholar 

  77. Acton, A., Banck, M., Bréfort, J., Cruz, M., Curtis, D., Hassinen, T., Heikkilä, V., Hutchison, G., Huuskonen, J., Jensen, J., Liboska, R., and Rowley, C. (2006) Chemical 2.00, Department of Chemistry, University of Kuopio: Kuopio, Finland, http://www.uku.fi/~thassine/projects/ghemical/.

  78. 78. Hassinen, T. and Peräkylä, M. (2001) New energy terms for reduced protein models implemented in an off-lattice force field. J Comput Chem, 22(12): 1229–1242.

    Article  CAS  Google Scholar 

  79. Hassinen, T., Hutchison, G., Cruz, M., Banck, M., Rowley, C., and Curtis, D. (2007) Ghemical-GMS 2.10, Department of Chemistry, University of Iowa.: Iowa City, IA, http://www.uiowa.edu/çghemical/ghemical.shtml.

  80. van Aalten, D. and Oswald, S. (2007) PRODRG 2, University of Dundee: Dundee, Scotland, http://davapc1.bioch.dundee.ac.uk/programs/prodrg/.

  81. 81. van Aalten, D.M., Bywater, R., Findlay, J.B., Hendlich, M., Hooft, R.W., and Vriend, G. (1996) PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J Comput Aided Mol Des, 10(3): 255–262.

    Article  PubMed  Google Scholar 

  82. 82. Schuttelkopf, A.W. and van Aalten, D.M. (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr, 60(Pt 8): 1355–1363.

    Article  PubMed  Google Scholar 

  83. Skillman, A.G. QUACPAC OpenEye Scientific Software: Santa Fe, NM, http://www. eyesopen.com/products/applications/quacpac.html.

  84. 84. Hetenyi, C. and van der Spoel, D. (2002) Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci, 11(7): 1729–1737.

    Article  CAS  PubMed  Google Scholar 

  85. 85. Raymer, M.L., Sanschagrin, P.C., Punch, W.F., Venkataraman, S., Goodman, E.D., and Kuhn, L.A. (1997) Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm. J Mol Biol, 265(4): 445–464.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This manuscript is TSRI publication number 18829. This work was supported by the National Institutes of Health (NIH) grant R01-GM069832.

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Authors and Affiliations

  1. Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA

    Garrett M. Morris

  2. BioSolveIT GmbH, Sankt Augustin,  , Germany

    Marguerita Lim-Wilby

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Andreas Kukol

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Morris, G.M., Lim-Wilby, M. (2008). Molecular Docking. In: Kukol, A. (eds) Molecular Modeling of Proteins. Methods Molecular Biology™, vol 443. Humana Press. https://doi.org/10.1007/978-1-59745-177-2_19

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  • DOI: https://doi.org/10.1007/978-1-59745-177-2_19

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  • Online ISBN: 978-1-59745-177-2

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