Journal of Computer-Aided Molecular Design

, Volume 27, Issue 3, pp 221–234 | Cite as

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

  • G. Madhavi Sastry
  • Matvey Adzhigirey
  • Tyler Day
  • Ramakrishna Annabhimoju
  • Woody ShermanEmail author


Structure-based virtual screening plays an important role in drug discovery and complements other screening approaches. In general, protein crystal structures are prepared prior to docking in order to add hydrogen atoms, optimize hydrogen bonds, remove atomic clashes, and perform other operations that are not part of the x-ray crystal structure refinement process. In addition, ligands must be prepared to create 3-dimensional geometries, assign proper bond orders, and generate accessible tautomer and ionization states prior to virtual screening. While the prerequisite for proper system preparation is generally accepted in the field, an extensive study of the preparation steps and their effect on virtual screening enrichments has not been performed. In this work, we systematically explore each of the steps involved in preparing a system for virtual screening. We first explore a large number of parameters using the Glide validation set of 36 crystal structures and 1,000 decoys. We then apply a subset of protocols to the DUD database. We show that database enrichment is improved with proper preparation and that neglecting certain steps of the preparation process produces a systematic degradation in enrichments, which can be large for some targets. We provide examples illustrating the structural changes introduced by the preparation that impact database enrichment. While the work presented here was performed with the Protein Preparation Wizard and Glide, the insights and guidance are expected to be generalizable to structure-based virtual screening with other docking methods.


Virtual screening Protein preparation Protein preparation wizard PrepWizard Docking Enrichment Ligand preparation Epik 

Supplementary material

10822_2013_9644_MOESM1_ESM.xls (86 kb)
Supplementary material 1 (XLS 86 kb)


  1. 1.
    Pierce AC, Jacobs M, Stuver-Moody C (2008) J Med Chem 51(6):1972CrossRefGoogle Scholar
  2. 2.
    Hao W, Hu Y, Niu C, Huang X, Chang CPB, Gibbons J, Xu J (2008) Bioorg Med Chem Lett 18(18):4988CrossRefGoogle Scholar
  3. 3.
    Salam NK, Huang TH-W, Kota BP, Kim MS, Li Y, Hibbs DE (2008) Chem Biol Drug Des 71(1):57Google Scholar
  4. 4.
    Kenyon V, Chorny I, Carvajal WJ, Holman TR, Jacobson MP (2006) J Med Chem 49(4):1356CrossRefGoogle Scholar
  5. 5.
    Li H, Huang J, Chen L, Liu X, Chen T, Zhu J, Lu W, Shen X, Li J, Hilgenfeld R (2009) J Med Chem 52(15):4936CrossRefGoogle Scholar
  6. 6.
    Shah F, Gut J, Legac J, Shivakumar D, Sherman W, Rosenthal PJ, Avery MA (2012) J Chem Inf Model 52(3):696CrossRefGoogle Scholar
  7. 7.
    Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Nat Rev Drug Disc 3(11):935CrossRefGoogle Scholar
  8. 8.
    Perola E, Walters WP, Charifson PS (2004) Proteins Struct Funct Bioinf 56(2):235CrossRefGoogle Scholar
  9. 9.
    Kellenberger E, Rodrigo J, Muller P, Rognan D (2004) Proteins Struct Funct Bioinf 57(2):225CrossRefGoogle Scholar
  10. 10.
    Sutherland JJ, Nandigam RK, Erickson JA, Vieth M (2007) J Chem Inf Model 47(6):2293CrossRefGoogle Scholar
  11. 11.
    McGaughey GB, Sheridan RP, Bayly CI, Culberson JC, Kreatsoulas C, Lindsley S, Maiorov V, Truchon J-F, Cornell WD (2007) J Chem Inf Model 47(4):1504CrossRefGoogle Scholar
  12. 12.
    Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S (2006) J Med Chem 49(20):5912CrossRefGoogle Scholar
  13. 13.
    Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C (2009) J Chem Inf Model 49(6):1455CrossRefGoogle Scholar
  14. 14.
    Stahl M, Rarey M (2001) J Med Chem 44(7):1035CrossRefGoogle Scholar
  15. 15.
    Schulz-Gasch T, Stahl M (2003) J Mol Model 9(1):47Google Scholar
  16. 16.
    Bissantz C, Folkers G, Rognan D (2000) J Med Chem 43(25):4759CrossRefGoogle Scholar
  17. 17.
    Cummings MD, DesJarlais RL, Gibbs AC, Mohan V, Jaeger EP (2005) J Med Chem 48(4):962CrossRefGoogle Scholar
  18. 18.
    Chen YZ, Zhi DG (2001) Proteins Struct Funct Bioinf 43(2):217CrossRefGoogle Scholar
  19. 19.
    Santiago DN, Pevzner Y, Durand AA, Tran M, Scheerer RR, Daniel K, Sung S-S, Lee Woodcock H, Guida WC, Brooks WH (2012) J Chem Inf Model 52(8):2192Google Scholar
  20. 20.
    Huggins DJ, Sherman W, Tidor B (2012) J Med Chem 55(4):1424CrossRefGoogle Scholar
  21. 21.
    Paul N, Kellenberger E, Bret G, Müller P, Rognan D (2004) Proteins Struct Funct Bioinf 54(4):671CrossRefGoogle Scholar
  22. 22.
    Feher M, Williams CI (2012) J Chem Inf Model 52(3):724CrossRefGoogle Scholar
  23. 23.
    Corbeil CR, Moitessier N (2009) J Chem Inf Model 49(4):997CrossRefGoogle Scholar
  24. 24.
    Santos R, Hritz J, Oostenbrink C (2009) J Chem Inf Model 50(1):146CrossRefGoogle Scholar
  25. 25.
    Repasky MP, Murphy RB, Banks JL, Greenwood JR, Tubert-Brohman I, Bhat S, Friesner RA (2012) J Comput Aided Mol Des 26(6):787Google Scholar
  26. 26.
    Goodsell DS, Olson AJ (1990) Proteins Struct Funct Bioinf 8(3):195CrossRefGoogle Scholar
  27. 27.
    Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE (1982) J Mol Biol 161(2):269CrossRefGoogle Scholar
  28. 28.
    Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) J Mol Biol 267(3):727CrossRefGoogle Scholar
  29. 29.
    Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) J Med Chem 47(7):1739CrossRefGoogle Scholar
  30. 30.
    Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD (2003) Proteins Struct Funct Genet 52(4):609CrossRefGoogle Scholar
  31. 31.
    Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL (2004) J Med Chem 47(7):1750CrossRefGoogle Scholar
  32. 32.
    Jain AN (2007) J Comput Aided Mol Des 21(5):281CrossRefGoogle Scholar
  33. 33.
    Verdonk ML, Berdini V, Hartshorn MJ, Mooij WTM, Murray CW, Taylor RD, Watson P (2004) J Chem Inf Comput Sci 44(3):793CrossRefGoogle Scholar
  34. 34.
    Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT (2006) J Med Chem 49(21):6177CrossRefGoogle Scholar
  35. 35.
    Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK (2008) J Mol Biol 377(3):914CrossRefGoogle Scholar
  36. 36.
    Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) J Comput Chem 19(14):1639CrossRefGoogle Scholar
  37. 37.
    Stroganov OV, Novikov FN, Stroylov VS, Kulkov V, Chilov GG (2008) J Chem Inf Model 48(12):2371CrossRefGoogle Scholar
  38. 38.
    Claussen H, Buning C, Rarey M, Lengauer T (2001) J Mol Biol 308(2):377CrossRefGoogle Scholar
  39. 39.
    Sherman W, Day T, Jacobson MP, Friesner RA, Farid R (2006) J Med Chem 49(2):534CrossRefGoogle Scholar
  40. 40.
    Nabuurs SB, Wagener M, de Vlieg J (2007) J Med Chem 50(26):6507CrossRefGoogle Scholar
  41. 41.
    Moitessier N, Therrien E, Hanessian S (2006) J Med Chem 49(20):5885CrossRefGoogle Scholar
  42. 42.
    Corbeil CR, Englebienne P, Moitessier N (2007) J Chem Inf Model 47(2):435CrossRefGoogle Scholar
  43. 43.
    Liu M, Bender SA, Cuny GD, Sherman W, Glicksman M, Ray SS (2013) Biochemistry (Mosc) 52(10):1725CrossRefGoogle Scholar
  44. 44.
    Beuming T, Sherman W (2012) J Chem Inf Model 52(12):3263CrossRefGoogle Scholar
  45. 45.
    Sherman W, Beard HS, Farid R (2006) Chem Biol Drug Des 67(1):83CrossRefGoogle Scholar
  46. 46.
    Osguthorpe DJ, Sherman W, Hagler AT (2012) J Phys Chem B 116(23):6952Google Scholar
  47. 47.
    Osguthorpe DJ, Sherman W, Hagler AT (2012) Chem Biol Drug Design 80(2):182Google Scholar
  48. 48.
    Cavasotto CN, Abagyan RA (2004) J Mol Biol 337(1):209CrossRefGoogle Scholar
  49. 49.
    Ferrari AM, Wei BQ, Costantino L, Shoichet BK (2004) J Med Chem 47(21):5076CrossRefGoogle Scholar
  50. 50.
    Broughton HB (2000) J Mol Graph Modell 18(3):247CrossRefGoogle Scholar
  51. 51.
    Rao S, Sanschagrin PC, Greenwood JR, Repasky MP, Sherman W, Farid R (2008) J Comput Aided Mol Des 22(9):621CrossRefGoogle Scholar
  52. 52.
    Salam NK, Nuti R, Sherman W (2009) J Chem Inf Model 49(10):2356CrossRefGoogle Scholar
  53. 53.
    1 K Drug-Like Ligand Decoys Set. Accessed 2012. Schrodinger, Inc.
  54. 54.
    Huang N, Shoichet BK, Irwin JJ (2006) J Med Chem 49(23):6789CrossRefGoogle Scholar
  55. 55.
    LigPrep v2.5. Portland, OR: Schrödinger, Inc.; 2011Google Scholar
  56. 56.
    Epik v2.2. Portland, OR: Schrödinger, Inc.; 2011Google Scholar
  57. 57.
    Shelley JC, Cholleti A, Frye LL, Greenwood JR, Timlin MR, Uchimaya M (2007) J Comput Aided Mol Des 21(12):681CrossRefGoogle Scholar
  58. 58.
    Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) J Mol Biol 112(3):535CrossRefGoogle Scholar
  59. 59.
    Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28(1):235CrossRefGoogle Scholar
  60. 60.
    Maestro v9.2. Portland, OR: Schrödinger, Inc.; 2011Google Scholar
  61. 61.
    Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, Friesner RA, Gallicchio E, Levy RM (2005) J Comput Chem 26:1752CrossRefGoogle Scholar
  62. 62.
    Jorgensen WL, Tirado-Rives J (1988) J Am Chem Soc 110:1657CrossRefGoogle Scholar
  63. 63.
    Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) J Phys Chem B 105(28):6474CrossRefGoogle Scholar
  64. 64.
    Shivakumar D, Williams J, Wu Y, Damm W, Shelley J, Sherman W (2010) J Chem Theory Comput 6(5):1509CrossRefGoogle Scholar
  65. 65.
    Österberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS (2002) Proteins Struct Funct Genet 46(1):34CrossRefGoogle Scholar
  66. 66.
    Rarey M, Kramer B, Lengauer T (1999) Proteins Struct Funct Bioinf 34(1):17CrossRefGoogle Scholar
  67. 67.
    Verdonk ML, Chessari G, Cole JC, Hartshorn MJ, Murray CW, Nissink JWM, Taylor RD, Taylor R (2005) J Med Chem 48(20):6504CrossRefGoogle Scholar
  68. 68.
    de Graaf C, Oostenbrink C, Keizers PHJ, van der Wijst T, Jongejan A, Vermeulen NPE (2006) J Med Chem 49(8):2417CrossRefGoogle Scholar
  69. 69.
    Myrianthopoulos V, Kritsanida M, Gaboriaud-Kolar N, Magiatis P, Ferandin Y, Durieu E, Lozach O, Cappel D, Soundararajan M, Filippakopoulos P, Sherman W, Knapp S, Meijer L, Mikros E, Skaltsounis A-L (2012) ACS Medicinal Chem Lett 4(1):22CrossRefGoogle Scholar
  70. 70.
    Beuming T, Che Y, Abel R, Kim B, Shanmugasundaram V, Sherman W (2011) Proteins Struct Funct Bioinf 80:871Google Scholar
  71. 71.
    Glide v5.7. Portland, OR: Schrödinger, Inc.; 2011Google Scholar
  72. 72.
    Truchon J-F, Bayly CI (2007) J Chem Inf Model 47(2):488CrossRefGoogle Scholar
  73. 73.
    Bird LE, Ren J, Wright A, Leslie KD, Degreve B, Balzarini J, Stammers DK (2003) J Biol Chem 278(27):24680Google Scholar
  74. 74.
    Nicholls A (2008) J Comput Aided Mol Des 22(3):239CrossRefGoogle Scholar
  75. 75.
    de Beer S, Vermeulen NPE, Oostenbrink C (2010) Curr Top Med Chem 10(1):55CrossRefGoogle Scholar
  76. 76.
    Katritch V, Jaakola V-P, Lane JR, Lin J, Ijzerman AP, Yeager M, Kufareva I, Stevens RC, Abagyan R (2010) J Med Chem 53(4):1799CrossRefGoogle Scholar
  77. 77.
    Huang N, Shoichet BK (2008) J Med Chem 51(16):4862CrossRefGoogle Scholar
  78. 78.
    Abel R, Young T, Farid R, Berne BJ, Friesner RA (2008) J Am Chem Soc 130(9):2817CrossRefGoogle Scholar
  79. 79.
    Young T, Abel R, Kim B, Berne BJ, Friesner RA (2007) PNAS 104:808CrossRefGoogle Scholar
  80. 80.
    Abel R, Salam NK, Shelley J, Farid R, Friesner RA, Sherman W (2011) ChemMedChem 6(6):1049CrossRefGoogle Scholar
  81. 81.
    Guimaraes CRW, Mathiowetz AM (2010) J Chem Inf Model 50(4):547CrossRefGoogle Scholar
  82. 82.
    Kalid O, Warshaviak DT, Shechter S, Sherman W, Shacham S (2012) J Comput Aided Mol Des 26(11):1217Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • G. Madhavi Sastry
    • 1
  • Matvey Adzhigirey
    • 2
  • Tyler Day
    • 2
  • Ramakrishna Annabhimoju
    • 1
  • Woody Sherman
    • 2
    Email author
  1. 1.SchrödingerHyderabadIndia
  2. 2.SchrödingerNew YorkUSA

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