12. Straatsma TP, McCammon JA (1992) Computational alchemy. Annu Rev Phys Chem
43:407–435
13. Tembe BL, McCammon JA (1984) Ligand-receptor interactions. Comput Chem 8:281–283
14. Rami Reddy M, Bacquet RJ, Zichi D, Matthews DA, Welsh KM et al (1992) Calculation of
solvation and binding free energy differences for folate-based inhibitors of the enzyme
thymidylate synthase. J Am Chem Soc 114:10117–10122
15. Wlodek ST, Antosiewicz J, McCammon JA, Straatsma TP, Gilson MK et al (1996) Binding
of tacrine and 6-chlorotacrine by acetylcholinesterase. Biopolymers 38:109–117
16. Marrone TJ, Straatsma TP, Briggs JM, Wilson DK, Quiocho FA, McCammon JA (1996)
Theoretical study of inhibition of adenosine deaminase by 8Rcoformycin and
8R-deoxycoformycin. J Med Chem 39:277–284
17. Damewood JR Jr (1996) Peptide mimetic design with the aid of computational chemistry.
Reviews in computational chemistry, In: Lipkowitz KB, Boyd DB (ed), vol 9. VCH
Publishers, New York, pp 1–79
18. Borman S (2005) Drug by design. C&EN, Washington, DC
19. Sumner JB (1926) The isolation and crystallization of the enzyme urease preliminary paper.
J Biol Chem 69(2):435–441
20. Sumner JB, Dounce AL (1937) Crystalline catalase. J Biol Chem 121(2):417–424
21. Northrop JH, Kunitz M, Herriott RM (1948) Crystalline Enzymes, Columbia Biological
Series, No. 12. Columbia University Press, New York, 16, p 305
22. Wlodawer A, Vondrasek J (1998) Inhibitors of HIV-1 protease: a major success of
structure-assisted drug design. Annu Rev Biophys Biomol Struct 27(1):249–284
23. Das K, Ding J, Hsiou Y, Clark AD, Moereels H, Koymans L, Andries K, Pauwels R,
Janssen PA, Boyer PL, Smith RH Jr, Kroeger Smith MB, Michejda CJ, Hughes SH,
Arnold E, Clark P (1996) Crystal structures of 8-Cl and 9-Cl TIBO complexed with
wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT
drug-resistant mutant. J Mol Biol 264(5):1085–1100
24. Hsiou Y, Das K, Ding J, Clark AD, Kleim JP, Rösner M, Winkler I, Riess G, Hughes SH,
Arnold E (1998). Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase
complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful
design feature for reducing drug resistance. J Mol Biol 284(2):313–323
25. Huang H, Chopra R, Verdine GL, Harrison SC (1998) Structure of a covalently trapped
catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science
282(5394):1669–1675
26. Ren J, Esnouf RM, Hopkins AL, Jones EY, Kirby I, Keeling J, Ross CK, Larder BA,
Stuart DI, Stammers DK (1998) 3′-Azido-3′-deoxythymidine drug resistance mutations in
HIV-1 reverse transcriptase can induce long range conformational changes. Proc Natl Acad
Sci 95(16):9518–9523
27. Sarafianos SG, Das K, Clark AD, Ding J, Boyer PL, Hughes SH, Arnold E (1999)
Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with
ß-branched amino acids. Proc Natl Acad Sci 96(18):10027–10032
28. Dickerson RE, Geis I (1983) Hemoglobin: structure, function, evolution, and pathology, vol
1983. Benjamin-Cummings Publishing Company
29. Williams DP, Naisbitt DJ (2002) Toxicophores: groups and metabolic routes associated with
increased safety risk. Curr Opin Drug Discov Devel 5(1):104–115
30. Aishima J, Owen RL, Axford D, Shepherd E, Winter G, Levik K, Gibbons P, Ashton A,
Evans G (2010) High-speed crystal detection and characterization using a fast-readout
detector. Acta Crystallogr Sect D: Biol Crystallogr 66(9):1032–1035
31. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM,
Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS,
Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4
suite and current developments. Acta Crystallogr Sect D: Biol Crystallogr 67(4):235–242
32. Walters WP, Stahl MT, Murcko MA (1998) Virtual screening—an overview. Drug Discov
Today 3(4):160–178
296
D. Velmurugan et al.
43:407–435
13. Tembe BL, McCammon JA (1984) Ligand-receptor interactions. Comput Chem 8:281–283
14. Rami Reddy M, Bacquet RJ, Zichi D, Matthews DA, Welsh KM et al (1992) Calculation of
solvation and binding free energy differences for folate-based inhibitors of the enzyme
thymidylate synthase. J Am Chem Soc 114:10117–10122
15. Wlodek ST, Antosiewicz J, McCammon JA, Straatsma TP, Gilson MK et al (1996) Binding
of tacrine and 6-chlorotacrine by acetylcholinesterase. Biopolymers 38:109–117
16. Marrone TJ, Straatsma TP, Briggs JM, Wilson DK, Quiocho FA, McCammon JA (1996)
Theoretical study of inhibition of adenosine deaminase by 8Rcoformycin and
8R-deoxycoformycin. J Med Chem 39:277–284
17. Damewood JR Jr (1996) Peptide mimetic design with the aid of computational chemistry.
Reviews in computational chemistry, In: Lipkowitz KB, Boyd DB (ed), vol 9. VCH
Publishers, New York, pp 1–79
18. Borman S (2005) Drug by design. C&EN, Washington, DC
19. Sumner JB (1926) The isolation and crystallization of the enzyme urease preliminary paper.
J Biol Chem 69(2):435–441
20. Sumner JB, Dounce AL (1937) Crystalline catalase. J Biol Chem 121(2):417–424
21. Northrop JH, Kunitz M, Herriott RM (1948) Crystalline Enzymes, Columbia Biological
Series, No. 12. Columbia University Press, New York, 16, p 305
22. Wlodawer A, Vondrasek J (1998) Inhibitors of HIV-1 protease: a major success of
structure-assisted drug design. Annu Rev Biophys Biomol Struct 27(1):249–284
23. Das K, Ding J, Hsiou Y, Clark AD, Moereels H, Koymans L, Andries K, Pauwels R,
Janssen PA, Boyer PL, Smith RH Jr, Kroeger Smith MB, Michejda CJ, Hughes SH,
Arnold E, Clark P (1996) Crystal structures of 8-Cl and 9-Cl TIBO complexed with
wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT
drug-resistant mutant. J Mol Biol 264(5):1085–1100
24. Hsiou Y, Das K, Ding J, Clark AD, Kleim JP, Rösner M, Winkler I, Riess G, Hughes SH,
Arnold E (1998). Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase
complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful
design feature for reducing drug resistance. J Mol Biol 284(2):313–323
25. Huang H, Chopra R, Verdine GL, Harrison SC (1998) Structure of a covalently trapped
catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science
282(5394):1669–1675
26. Ren J, Esnouf RM, Hopkins AL, Jones EY, Kirby I, Keeling J, Ross CK, Larder BA,
Stuart DI, Stammers DK (1998) 3′-Azido-3′-deoxythymidine drug resistance mutations in
HIV-1 reverse transcriptase can induce long range conformational changes. Proc Natl Acad
Sci 95(16):9518–9523
27. Sarafianos SG, Das K, Clark AD, Ding J, Boyer PL, Hughes SH, Arnold E (1999)
Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with
ß-branched amino acids. Proc Natl Acad Sci 96(18):10027–10032
28. Dickerson RE, Geis I (1983) Hemoglobin: structure, function, evolution, and pathology, vol
1983. Benjamin-Cummings Publishing Company
29. Williams DP, Naisbitt DJ (2002) Toxicophores: groups and metabolic routes associated with
increased safety risk. Curr Opin Drug Discov Devel 5(1):104–115
30. Aishima J, Owen RL, Axford D, Shepherd E, Winter G, Levik K, Gibbons P, Ashton A,
Evans G (2010) High-speed crystal detection and characterization using a fast-readout
detector. Acta Crystallogr Sect D: Biol Crystallogr 66(9):1032–1035
31. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM,
Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS,
Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4
suite and current developments. Acta Crystallogr Sect D: Biol Crystallogr 67(4):235–242
32. Walters WP, Stahl MT, Murcko MA (1998) Virtual screening—an overview. Drug Discov
Today 3(4):160–178
296
D. Velmurugan et al.