33. Bajorath J (2002) Integration of virtual and high-throughput screening. Nat Rev Drug
Discov 1(11):882–894
34. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE (1982) A geometric approach to
macromolecule-ligand interactions. J Mol Biol 161(2):269–288
35. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual
screening for drug discovery: methods and applications. Nat Rev Drug Discov 3(11):
935–949
36. Connolly ML (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221
(4612):709–713
37. Connolly ML (1983) Analytical molecular surface calculation. J Appl Crystallogr 16
(5):548–558
38. Goodford PJ (1985) A computational procedure for determining energetically favorable
binding sites on biologically important macromolecules. J Med Chem 28(7):849–857
39. Goodsell DS, Lauble H, Stout CD, Olson AJ (1993) Automated docking in crystallography:
analysis of the substrates of aconitase. Proteins: Struct, Funct, Bioinf 17(1):1–10
40. Chemical Computing Group. MOE (2003) Montreal. Quebec, Canada
41. GOLD Version 1.2. [online] 2003. http://www.ccdc.cam.ac.uk/products/life_sciences/gold/
42. Westhead DR, Clark DE, Murray CW (1997) A comparison of heuristic search algorithms
for molecular docking. J Comput Aided Mol Des 11(3):209–228
43. Ewing TJ, Makino S, Skillman AG, Kuntz ID (2001) DOCK 4.0: search strategies for
automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 15
(5):411–428
44. Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an
incremental construction algorithm. J Mol Biol 261(3):470–489
45. 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) Glide: a new
approach for rapid, accurate docking and scoring. 1. Method and assessment of docking
accuracy. J Med Chem 47(7):1739–1749
46. Welch W, Ruppert J, Jain AN (1996) Hammerhead: fast, fully automated docking of flexible
ligands to protein binding sites. Chem Biol 3(6):449–462
47. Kearsley SK, Underwood DJ, Sheridan RP, Miller MD (1994) Flexibases: a way to enhance
the use of molecular docking methods. J Comput Aided Mol Des 8(5):565–582
48. Knegtel RM, Kuntz ID, Oshiro CM (1997) Molecular docking to ensembles of protein
structures. J Mol Biol 266(2):424–440
49. Kramer B, Rarey M, Lengauer T (1999) Evaluation of the FLEXX incremental construction
algorithm for protein–ligand docking. Proteins: Struct, Funct, Bioinf 37(2):228–241
50. Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD (2003) Improved protein–
ligand docking using GOLD. Proteins: Struct, Funct, Bioinf 52(4):609–623
51. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998)
Automated docking using a Lamarckian genetic algorithm and an empirical binding free
energy function. J Comput Chem 19(14):1639–1662
52. Böhm HJ (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
53. Böhm HJ (1998) Prediction of binding constants of protein ligands: a fast method for the
prioritization of hits obtained from de novo design or 3D database search programs.
J Comput Aided Mol Des 12(4):309–323
54. Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) Empirical scoring
functions: I. The development of a fast empirical scoring function to estimate the binding
affinity of ligands in receptor complexes. J Comput Aided Mol Des 11(5):425–445
55. Wang R, Liu L, Lai L, Tang Y (1998) SCORE: a new empirical method for estimating the
binding affinity of a protein-ligand complex. J Mol Model 4(12):379–394
56. Tao P, Lai L (2001) Protein ligand docking based on empirical method for binding affinity
estimation. J Comput Aided Mol Des 15(5):429–446
Structure-Based Drug Design…
297
Discov 1(11):882–894
34. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE (1982) A geometric approach to
macromolecule-ligand interactions. J Mol Biol 161(2):269–288
35. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual
screening for drug discovery: methods and applications. Nat Rev Drug Discov 3(11):
935–949
36. Connolly ML (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221
(4612):709–713
37. Connolly ML (1983) Analytical molecular surface calculation. J Appl Crystallogr 16
(5):548–558
38. Goodford PJ (1985) A computational procedure for determining energetically favorable
binding sites on biologically important macromolecules. J Med Chem 28(7):849–857
39. Goodsell DS, Lauble H, Stout CD, Olson AJ (1993) Automated docking in crystallography:
analysis of the substrates of aconitase. Proteins: Struct, Funct, Bioinf 17(1):1–10
40. Chemical Computing Group. MOE (2003) Montreal. Quebec, Canada
41. GOLD Version 1.2. [online] 2003. http://www.ccdc.cam.ac.uk/products/life_sciences/gold/
42. Westhead DR, Clark DE, Murray CW (1997) A comparison of heuristic search algorithms
for molecular docking. J Comput Aided Mol Des 11(3):209–228
43. Ewing TJ, Makino S, Skillman AG, Kuntz ID (2001) DOCK 4.0: search strategies for
automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 15
(5):411–428
44. Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an
incremental construction algorithm. J Mol Biol 261(3):470–489
45. 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) Glide: a new
approach for rapid, accurate docking and scoring. 1. Method and assessment of docking
accuracy. J Med Chem 47(7):1739–1749
46. Welch W, Ruppert J, Jain AN (1996) Hammerhead: fast, fully automated docking of flexible
ligands to protein binding sites. Chem Biol 3(6):449–462
47. Kearsley SK, Underwood DJ, Sheridan RP, Miller MD (1994) Flexibases: a way to enhance
the use of molecular docking methods. J Comput Aided Mol Des 8(5):565–582
48. Knegtel RM, Kuntz ID, Oshiro CM (1997) Molecular docking to ensembles of protein
structures. J Mol Biol 266(2):424–440
49. Kramer B, Rarey M, Lengauer T (1999) Evaluation of the FLEXX incremental construction
algorithm for protein–ligand docking. Proteins: Struct, Funct, Bioinf 37(2):228–241
50. Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD (2003) Improved protein–
ligand docking using GOLD. Proteins: Struct, Funct, Bioinf 52(4):609–623
51. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998)
Automated docking using a Lamarckian genetic algorithm and an empirical binding free
energy function. J Comput Chem 19(14):1639–1662
52. Böhm HJ (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
53. Böhm HJ (1998) Prediction of binding constants of protein ligands: a fast method for the
prioritization of hits obtained from de novo design or 3D database search programs.
J Comput Aided Mol Des 12(4):309–323
54. Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) Empirical scoring
functions: I. The development of a fast empirical scoring function to estimate the binding
affinity of ligands in receptor complexes. J Comput Aided Mol Des 11(5):425–445
55. Wang R, Liu L, Lai L, Tang Y (1998) SCORE: a new empirical method for estimating the
binding affinity of a protein-ligand complex. J Mol Model 4(12):379–394
56. Tao P, Lai L (2001) Protein ligand docking based on empirical method for binding affinity
estimation. J Comput Aided Mol Des 15(5):429–446
Structure-Based Drug Design…
297