Protein structure evaluation using an all-atom energy based empirical scoring function

Journal of Biomolecular Structure and Dynamics

Volumn 23, Issue 4, 2006, Pages 385-406

  Narang, Pooja ^a   Bhushan, Kumkum ^a   Bose, Surojit ^a   Jayaram, B ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY DELHI   (India)

Author keywords

Biomolecular modeling; Decoys; Physics based potentials; Protein tertiary structure; Scoring function

Indexed keywords

ALPHA GLOBULAR PROTEIN; BETA GLOBULAR PROTEIN; GLOBULAR PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; INTERNET; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY;

EID: 30744462062     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2006.10531234     Document Type: Article

References (105)

1. Kollman, P., 1993. Chem. Rev., 93:2395–2417.
2. Jorgensen, W., 1989. Acc. Chem. Res., 22:184–189.
3. van Gunsteren, W. F., and Berendsen, H. J. C., 1990. Angew. Chem. Int. Ed. Engl., 29:992–1023.
4. McCammon, J. A., 1991. Curr. Opin. Struct. Biol., 1:196–200.
5. Beveridge, D. L., and DiCapua, F. M., 1989. Annu. Rev. Biophys. Biomol. Struct., 18:431–492.
6. Jayaram, B., Liu, Y., and Beveridge, D. L., 1998. J. Chem. Phys., 109:1465–1471.
7. Jayaram, B., Sprous, D., and Beveridge, D. L., 1998. J. Phys. Chem. B, 102:9571–9576.
8. Kalra, P., Reddy, T. V., and Jayaram, B., 2001. J. Med. Chem., 44:4325–4338.
9. Jayaram, B., Sprous, D., Young, M. A., and Beveridge, D. L., 1998. J. Am. Chem. Soc., 120:10629–10633.
10. Latha, N., Jain, T., Sharma, P., and Jayaram, B., 2004. J. Biomol. Struct. Dynam., 21:791–804.
11. Latha, N., and Jayaram, B., 2005. Drug Design Reviews—Online, 2:145–165.
12. Brooks III, C. L., 2002. Proc. Natl. Acad. Sci. USA, 99:1099–1100.
13. Shea, J. E., and Brooks, C. L., III. 2001. Annu. Rev. Phys. Chem., 52:499–535.
14. Brooks III, C. L., 2002. Nature, 420:33–34.
15. Brockwell, D. J., Smith, D. A., and Radford, S. E., 2000. Curr. Opin. Struct. Biol., 10:16–25.
16. Day, R., and Daggett, V., 2003. Adv. Protein Chem., 66:373–403.
17. Dill, K. A., and Chan, H. S., 1997. Nat. Struct. Biol., 4:10–19.
18. Dill, K. A., 1993. Curr. Opin. Struct. Biol., 3:99–103.
19. Yue, K., and Dill, K. A., 1996. Protein Sci., 5:254–261.
20. Betancourt, M. R., and Skolnick, J., 2001. J. Comp. Chem., 22:339–353.
21. Zhang, Y., and Skolnick, J., 2004. Biophys. J., 87:2647–2655.
22. Zhang, Y., and Skolnick, J., 2004. Proc. Natl. Acad. Sci. USA, 101:7594–7599.
23. Fetrow, J. S., Giammona, A., Kolinski, A., and Skolnick, J., 2002. Curr. Pharm. Biotechnol., 3:329347
24. Monge, A., Lathrop, J. P., Gunn, J. R., Shenkin, P. S., and Friesner, R. A., 1995. J. Mol. Biol., 247:995–1012.
25. Andrec, M., Harano, Y., Jacobson, M. P., Friesner, R. A., and Levy, R. M., 2002. J. Struct. Funct. Genomics, 2:103–111.
26. Friesner, R. A., and Gunn, J. R., 1996. Annu Rev. Biophys. Biomol. Struct., 25:315–342.
27. Hardin, C., Pogorelov, T. V., and Luthey-Schulten, Z., 2002. Curr. Opin. Struct. Biol., 12:176–181.
28. Honig, B., 1999. J. Mol. Biol., 293:283–293.
29. Lazaridis, T., and Karplus, M., 2003. Biophys. Chem., 100:367–395.
30. Levitt, M., Gerstein, M., Huang, E., Subbiah, S., and Tsai, J., 1997. Annu. Rev. Biochem., 66:549–579.
31. Moult, J., 1999. Curr. Opin. Biotechnol., 10:583–588.
32. Osguthorpe, D. J., 2000. Curr. Opin. Struct. Biol., 10:146–152.
33. Radford, S. E., 2000. Trends Biochem. Sci., 25:611–618.
34. Srinivasan, R., Fleming, P. J., and Rose, G. D., 2004. Methods. Enzymol., 383:48–66.
35. Srinivas, G., and Bagchi, B., 2002. Curr. Sci., 82:179–185.
36. Mukherjee, A., and Bagchi, B., 2003. J. Chem. Phys., 118:4733–4747.
37. Zwanzig, R., Szabo, A., and Bagchi, B., 1992. Proc. Natl. Acad. Sci. USA, 89:20–22.
38. Mukherjee, A., and Bagchi, B., 2003. Proc. Indian Acad. Sci., 115:621–636.
39. Tsai, C. J., Ma, B., Kumar, S., Sham, Y., Wolfson, H., and Nussionv, R., 2001. IBM J. Res. Dev., 45:513–23.
40. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferugson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A., 1995. J. Am Chem. Soc., 117:5179–5197.
41. Brooks, B. R., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S., and Karplus, M., 1983. J. Comput. Chem., 4:187–217.
42. Tirado-Rives, J., and Jorgensen, W. L., 1993. Biochemistry, 16:4175–4184.
43. van Gunsteren, W. F., Billeter, S. R., Eising, A. A., Hünenberger, P. H., Krüger, P., Mark, A. E., Scott, W. R. P., and Tironi, L. G., 1996. Biomolecular Simulation:The GROMOS96 Manual and User Guide. BIOMOS b.v.:Zürich.
44. Moult, J., 1997. Curr. Opin. Struct. Biol., 7:194–199.
45. Alexander, D., and Mackerell, A. D., Jr. 2004. J. Comput. Chem., 25:1584–1604.
46. MacKerell, A. D., Jr., Feig, M., and Brooks, C. L., III. 2004. J. Am. Chem. Soc., 126:698–699.
47. Rooman, M. J., and Wodak, S. J., 1995. Protein Eng., 8:849–858.
48. Clementi, C., Vendruscolo, M., Maritan, A., and Domany, E., 1999. Proteins:Struct. Funct. Genet., 37:544–553.
49. Godzik, A., 1996. Structure, 4:363–366.
50. Vajda, S., Sippl, M., and Novotny, J., 1997. Curr. Opin. Struct. Biol., 7:222–228.
51. Dominy, B. N., and Shakhnovich, E. I., 2004. J. Med. Chem., 47:4538–4558.
52. Shimada, J., Ischenko, A. I., and Shakhnovich, E. I., 2000. Protein Sci., 9:765–775.
53. Lazaridis, T., and Karplus, M., 2000. Curr. Opin. Struct. Biol., 10:139–145.
54. Sippl, M. J., 1995. Curr. Opin. Struct. Biol., 5:229–235.
55. Lu, H., and Skolnick, J., 2001. Proteins:Struct. Funct. Genet., 44:223–232.
56. Jernigan, R. L., and Bahar, I., 1996. Curr. Opin. Struct. Biol., 6:195–209.
57. Pillardy, J., Czaplewski, C., Liwo, A., Wedemeyer, W. J., Lee, J., Ripoll, D. R., Arlukowicz, P., Oldziej, S., Arnautova, Y. A., and Scheraga, H. A., 2001. J. Phys. Chem. B, 105:7299–7311.
58. Mohanty, D., Dominy, B. N., Kolinski, A., Brooks, C. L., III and Skolnick, J., 1999. Proteins:Struct. Funct. Genet., 35:447–452.
59. Park, B., and Levitt, M., 1996. J. Mol. Biol., 258:367–392.
60. Bahar, I., and Jernigan, R. L., 1997. J. Mol. Biol., 266:195–214.
61. Fain, B., Xia, Y., and Levitt, M., 2001. IBM J. Res. & Dev., 45:525–532.
62. McConkey, B. J., Sobolev, V., and Edelman, M., 2003. Proc. Natl. Acad. Sci. USA, 100:3215–3220.
63. Huang, E. S., Subbiah, S., Tsai, J., and Levitt, M., 1996. J. Mol. Biol., 257:716–725.
64. Huang, E. S., Samudrala, R., and Ponder, J. W., 1999. J. Mol. Biol., 290:267–281.
65. Berglund, A., Head, R. D., Welsh, E. A., and Marshall, G. R., 2004. Proteins:Struct. Funct. Bioinfo., 54:289–302.
66. Lazaridis, T., and Karplus, M., 1998. J. Mol. Biol., 288:477–487.
67. Petrey, D., and Honig, B., 2000. Protein Sci., 9:2181–2191.
68. Gatchell, D. W., Dennis, S., and Vajda, S., 2000. Proteins:Struct. Funct. Genet., 41:518–534.
69. Lee, M. R., and Kollman, P. A., 2001. Structure, 9:905–916.
70. Dominy, B. N., and L. Brooks, C., III. 2002. J. Comput. Chem., 23:147–160.
71. Felts, A. K., Gallicchio, E., Wallqvist, A., and Levy, R. M., 2002. Proteins:Struct. Funct. Genet., 48:404–422.
72. Zhu, J., Zhu, Q. I., Shi, Y., and Liu, H., 2003. Proteins:Struct. Funct. Genet., 52:598–608.
73. Tsai, J., Bonneau, R., Morozov, A. V., Kuhlman, B., Rohl, C. A., and Baker, D., 2003. Proteins:Struct. Funct. Genet., 53:76–87.
74. Lee, M. C., and Duan, Y., 2004. Proteins:Struct. Funct. Bioinfo., 55:620–634.
75. Hsieh, M. J., and Luo, R., 2004. Proteins:Struct. Funct. Bioinfo., 56:475–486.
76. Arora, N., and Jayaram, B., 1998. J. Phys. Chem., 102:6139–6144.
77. Arora, N., and Jayaram, B., 1997. J. Comp. Chem., 18:1245–1252.
78. Hingerty, B. E., Ritchie, R. H., Ferreli, T. L., and Turner, J. E., 1985. Biopolymers, 24:427–439.
79. Ramstein, J., and Lavery, R., 1988. Proc. Natl. Acad. Sci. USA, 85:7231–4235.
80. Jayaram, B., Swaminathan, S., and Beveridge, D. L., 1990. Macromolecules, 23:3156–3165.
81. Jayaram, B., and Beveridge, D. L., 1990. J. Phys. Chem., 94:4666–4671.
82. Ramanathan, P. S., and Friedman, H. L., 1971. J. Chem. Phys., 54:1086–1099.
83. Friedman, H. L., and Krishnan, C. V., 1973. J. Soln. Chem., 2:119–140.
84. Hodes, Z. I., Nemethy, G., and Scheraga, H. A., 1979. Biopolymers, 18:1565–1610.
85. Hopfinger, A. J., 1973. Conformational Properties of Macromolecules. New York:Academic Press.
86. Jayaram, B., Ravishanker, G., and Beveridge, D. L., 1988. J. Phys. Chem., 92:1032–1034.
87. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L., 1983. J. Chem. Phys., 79:926–935.
88. Plaxco, K. W., and Goddard, W. A., III. 1994. Biochemistry, 33:3050–3054.
89. Jayaram. In, B., 1995. Proceedings of the Ninth Conversation in Biomolecular Structure and Dynamics. Edited by:Sarma, R. H., New York:Adenine Press. J. Biol. Struct. Dynam. 1, 109 (1996).
90. Young, M. A., Jayaram, B., and Beveridge, D. L., 1998. J Phys. Chem., 102:7666–7669.
91. Schwede, T., Kopp, J., Guex, N., and Peitsch, M. C., 2003. Nucleic Acids Res., 31:3381–3385.
92. Guex, N., and Peitsch, M. C., 1997. Electrophoresis, 18:2714–2723.
93. Peitsch, M. C., 1995. Bio/Technology, 13:658–660.
94. Lambert, C., Leonard, N., Bolle De, X., and Depiereux, E., 2002. Bioinformatics, 18:1250–1256.
95. Bates, P. A., Kelley, L. A., MacCallum, R. M., and Sternberg, M. J. E., 2001. Protein:Struct. Funct. Genet. Suppl., 5:39–46.
96. Lund, O., Nielsen, M., Lundegaard, C., and Worning, P., 2002. Abstract at the CASP5 Conference A102
97. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. R., Chetham, T. A., III. 1995. Comp. Phys. Commun., 91:1–41.
98. Narang, P., Bhushan, K., Bose, S., and Jayaram, B., 2005. Phys. Chem. Chem. Phys., 7:2364–2375.
99. Holm, L., and Sander, C., 1992. J. Mol. Biol., 225:93–105.
100. Xia, Y., Huang, E. S., Levitt, M., and Samudrala, R., 2000. J. Mol. Biol., 300:171–185.
101. Keasar, C., and Levitt, M., 2003. J. Mol. Biol., 329:159–174.
102. Simons, K. T., Kooperberg, C., Huang, E. S., and Baker, D., 1997. J. Mol. Biol., 268:209–225.
103. Samudrala, R., and Levitt, M., 2002. BMC Struct. Biol., 2:3–10.
104. Simons, K. T., Bonneau, R., Ruczinski, I., and Baker, D., 1999. Proteins:Struct. Funct. Genet. Suppl, 3:171–176.
105. Wang, K., Fain, B., Levitt, M., and Samudrala, R., 2004. BMC Structural Biology, 4:1–18.