Computational methods for the prediction of protein folds

Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology

Volumn 1343, Issue 1, 1997, Pages 1-15

  Dandekar, Thomas ^a   König, Rainer ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL NEURAL NETWORK; COMPUTER MODEL; ENERGY; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW;

ANIMALS; COMPUTER SIMULATION; HUMANS; MODELS, MOLECULAR; MODELS, THEORETICAL; PREDICTIVE VALUE OF TESTS; PROTEIN FOLDING;

EID: 0345019895     PISSN: 01674838     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-4838(97)00132-5     Document Type: Review

References (160)

1. MacArthur M., Discroll P.C., Thornton J.M. Trends Biotechnol. 12:1994;149-153.
2. Moult J. Curr. Op. Biotech. 7:1996;422-427.
3. Levinthal C. J. Chem. Phys. 65:1968;44-45.
4. Sali A., Schakhnovich E., Karplus M. Nature. 369:1994;248-251.
5. Bryngelson J.D., Onuchic J.N., Socci N.D., Wolynes P.G. Proteins: Structure, Function and Genetics. 21:1995;167-195.
6. Yun-Yu S., Mark A.E., Cun-xin W., Fuhuae H., Berendsen H.J.C., van Gunsteren W.F. Protein Eng. 6:1993;289-295.
7. Scheraga H.A. Biophys. Chem. 59:1996;329-339.
8. Defay T., Cohen F.E. Proteins. 23:1995;431-445.
9. Mosimann S., Meleshko R., James M.N.G. Proteins. 23:1995;301-317.
10. Lemer C.M.R., Rooman M.J., Wodak S.J. Proteins. 23:1995;337-355.
11. Bai Y., Englander S.W. Proteins: Structure, Function and Genetics. 24:1996;145-151.
12. Anfinsen C.B. Science. 181:1973;223-230.
13. T. Creighton, Protein Folding, Freeman, New York, 1992.
14. Gething M.J., Sambrook J. Nature. 355:1992;33-45.
15. Hartl F.U. Nature. 371:1994;557-559.
16. Ngo T.J., Marks J. Protein Eng. 5:1992;313-321.
17. Lathrop R.H. Protein Eng. 7:1994;1059-1068.
18. Davis M.E., McCammon J.A. Chem. Rev. 90:1990;509-521.
19. Juffer A.H., Botta E.F.F., van Keulen B.A.M., van der Ploeeg A., Berendsen H.J.C. J. Comp. Phys. 97:1991;144-171.
20. Holst M., Kozack R.E., Saied F., Subramaniam S. J. Biomol. Struct. Dyn. 11:1994;1437-1445.
21. Nemethy G., Gibson K.D., Palmer K.A., Yoon C.N., Paterlini G., Zagari A., Rumsey S., Scheraga H.A. J. Phys. Chem. 96:1992;6472-6484.
22. van Gunsteren W.F., Berendsen H.J.C. Angew. Chem., Int. Ed. Engl. 29:1990;992-1023.
23. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. J. Comp. Chem. 4:1983;187-217.
24. Weiner S.J., Kollman P.A., Nguyen D.T., Case D.A. J. Comp. Chem. 7:1986;230.
25. Dauber-Osguthorpe P., Roberts V.A., Osguthorpe D.J., Wolff J., Genest M., Hagler A.T. Proteins. 4:1988;31-47.
26. Robson B., Platt E. J. Mol. Biol. 188:1986;259-281.
27. Still W.C., Tempzczyk A., Hawley R.C., Hendrickson T. J. Am. Chem. Soc. 112:1990;6127-6129.
28. Cramer C.J., Truhlar D.G. Science. 256:1992;213-217.
29. Abagyan R., Totrov M. J. Mol. Biol. 235:1994;983-1002.
30. Steinbach P.J., Brooks B.R. J. Comp. Chem. 15:1994;667-683.
31. Ding H.Q., Karasawa N., Goddard W.A. III J. Chem. Phys. 97:1992;4309-4315.
32. Schreiber H., Steinhäuser O. J. Mol. Biol. 228:1992;909-923.
33. Richardson J.S., Richardson D.C., Tweedy N.B., Gernet K.M., Quinn T.P., Hecht M.H., Ericson B.W., Yan Y., McClain R.D., Donlan M.E., Surles M.C. Biophys. J. 63:1992;1186-1209.
34. Dandekar T., Argos P. J. Mol. Biol. 236:1994;844-861.
35. Aszodi A., Taylor W.R. Folding and Design. 1:1996;325-334.
36. Sun S. Protein Sci. 2:1993;762-785.
37. Wallqvist A., Ullner M. Proteins. 18:1994;267-280.
38. Aszodi A., Taylor W.R. Biopolymers. 34:1994;489-505.
39. Sippl M.J. Curr. Op. Struct. Biol. 5:1995;229-235.
40. Sippl M.J., Weitckus S. Proteins. 13:1992;258-271.
41. Lund O., Harsen J., Brunak S., Bohr J. Protein Sci. 5:1996;2217-2225.
42. Godzik A., Kolinski A., Skolnick J. J. Comp. Chem. 14:1993;1194-1202.
43. Brown W.J., North A.C.T., Phillips D.C., Brew K., Vanaman T.C., Hill R.A. J. Mol. Biol. 42:1969;65-86.
44. Johnson M.S., Srinivasan N., Sowdhamini R., Blundell T.L. Crit. Rev. Biochem. Mol. Biol. 29:1994;1-68.
45. Holm L., Sander C. Nucl. Acid Res. 22:1994;3600-3609.
46. Taylor W.R., Orengo C.A. J. Mol. Biol. 208:1989;1-22.
47. Flores T.P., Orengo C.A., Moss D.S., Thornton J.M. Protein Sci. 2:1993;1811-1826.
48. Luo Y., Lai L., Xu X., Tang Y. Protein Eng. 6:1993;373-376.
49. May A.C.W., Johnson M.S. Protein Eng. 7:1994;475-485.
50. van Gelder C.W.G., Leusen F.J.J., Leunissen J.A.M., Noordik J.H. Proteins. 18:1994;174-185.
51. Topham C.M., McLeod A., Eisenmenger F., Overington J.P., Johnson M.S., Blundell T.L. J. Mol. Biol. 229:1993;194-220.
52. Hubbard S.J., Eisenmenger F., Thornton J.M. Protein Sci. 3:1994;757-768.
53. Laughton C.A. J. Mol. Biol. 235:1994;1088-1097.
54. Dunbrack R.L., Karplus M. Nature Struct. Biol. 1:1994;334-340.
55. Vriend G. J. Mol. Graph. 8:1990;52-56.
56. Sali A., Blundell T.L. J. Mol. Biol. 234:1993;779-815.
57. De Fillipis V., Sander C., Vriend G. Protein Eng. 7:1994;1203-1208.
58. Nordhoff A., Bücheler U.S., Werner D., Schirmer R.H. Biochemistry. 32:1993;4060-4066.
59. Schneider R., Sander C. Nucleic Acids Res. 24:1996;201-205.
60. Desmet J., DeMayer M., Hazes B., Lasters I. Nature. 356:1992;539-542.
61. Lasters I., DeMaeyer M., Desmet J. Protein Eng. 8:1995;815-822.
62. Renouf D.V., Hounsell E.F. Adv. Exp. Med. Biol. 376:1995;37-45.
63. Sonnhammer E.L.L., Durbin R. Comput. Appl. Biosci. 10:1994;301-307.
64. Chothia C., Lesk A.M. EMBO J. 5:1986;823-826.
65. Henikoff S., Henikoff J.G. J. Mol. Biol. 243:1994;574-578.
66. Gibson T.J., Hyvönen M., Musacchio A., Saraste M., Birney E. Trends Biochem. Sci. 19:1994;349-353.
67. Bairoch A. Nucl. Acids. Res. 21:1993;3097-3103.
68. Attwood T.K., Beck M.E. Protein Eng. 7:1994;841-848.
69. Frishman D.I., Argos P. J. Mol. Biol. 228:1992;951-962.
70. Chandonia J.M., Karplus M. Protein Sci. 4:1995;275-285.
71. Rost B. Methods Enzymol. 266:1996;525-539.
72. Rost B., Sander C. Proteins. 23:1995;295-300.
73. Frishman D. Biochem. Biophys. Res. Commun. 219:1996;686-689.
74. Reczko M., Martin A.C., Bohr H., Suhai S. Protein Eng. 8:1995;389-395.
75. Rohde K., Bork P. Comput. Appl. Biosci. 9:1993;183-189.
76. Bork P., Gibson T. Methods Enzymol. 266:1996;162-184.
77. Bork P., Blomberg N., Nilges M. Nat. Genet. 13:1996;22-23.
78. Bork P. Science. 271:1996;1431-1432.
79. Dubchak I., Holbrook S.R., Kim H.S. Proteins. 16:1993;79-91.
80. Reczko M., Bohr H. Nucl. Acids Res. 22:1994;3616-3619.
81. Dubchak I., Muchnik I., Holbrook S.R., Kim S.H. PNAS. 92:1995;8700-8704.
82. Casari G., Sander G., Valencia A. Nat. Struct. Biol. 2:1995;171-178.
83. Persson B., Argos P. Protein Sci. 5:1996;363-371.
84. Alexandrov N.N., Go N. Protein Sci. 3:1994;866-875.
85. Crippen G.M., Maiorov V.N. J. Mol. Biol. 252:1995;144-151.
86. Zhang K.Y.J., Eisenberg D. Protein Sci. 3:1994;687-695.
87. Ouzounis C., Sander C., Scharf M., Schneider R. J. Mol. Biol. 232:1993;805-825.
88. Gracy J., Chiche L., Sallantin J. Protein Eng. 6:1993;821-829.
89. Abagyan R., Frishman D.I., Argos P. Proteins. 19:1994;132-140.
90. Bryant S.H., Lawrence C.E. Proteins. 16:1993;92-112.
91. Johnson D.T., Thornton J.M. Curr. Op. Struct. Biol. 6:1996;210-216.
92. Bowie J.U., Zhang K., Wilmanns M., Eisenberg D. Methods Enzymol. 266:1996;598-616.
93. Bowie J.U., Luthy R., Eisenberg D. Science. 253:1991;164-170.
94. Koehl P., Delarue M. Proteins. 20:1994;264-278.
95. Colovos C., Yeates T.O. Protein Sci. 2:1993;1511-1519.
96. Maiorov V.N., Crippen G.M. J. Mol. Biol. 227:1992;876-888.
97. Jones D.T. Protein Sci. 3:1994;567-574.
98. Thomas P.D., Dill K.A. J. Mol. Biol. 257:1996;457-469.
99. Jones D.T., Thornton J.M. Curr. Op. Struct. Biol. 6:1996;210-216.
100. Novotny J., Bruccoleri R., Newell J., Murphy D., Haber E., Karplus M. J. Biol. Chem. 258:1983;14433-14437.
101. Jones D.T., Miller R.T., Thornton J.M. Proteins. 23:1995;387-397.
102. Russel R.B., Barton G.J. J. Mol. Biol. 244:1994;332-350.
103. Wang Y., Zhang H., Li W., Scott RA PNAS. 92:1995;709-713.
104. Jin L., Cohen F.E., Wells J.A. Proc. Natl. Acad. Sci. 91:1994;113-117.
105. Finkelstein A.V., Reva B. Nature. 351:1991;497-499.
106. Unger R., Moult J. J. Mol. Biol. 231:1993;75-81.
107. Bruccoleri R.E. Mol. Simul. 10:1993;151-174.
108. Cohen B.I., Presnell S.R., Cohen F.E. Protein Sci. 2:1993;2134-2145.
109. Olszewsky K.A., Piela L., Scheraga H.A. J. Phys. Chem. 96:1992;4672-4676.
110. Kostrowicki J., Scheraga H.A. J. Phys. Chem. 96:1992;7442-7449.
111. Shalloway D. J. Glob. Optim. 2:1992;281-311.
112. Head-Gordon T., Stillinger F.H. Biopolymers. 33:1993;292-303.
113. Clark D.A., Rawlings C.J., Shirazi J., Veron A., Reeve M. Ismb. 1:1993;83-91.
114. Nilges M. J. Mol. Biol. 245:1995;645-660.
115. Sibbald P. J. Theo. Biol. 173:1995;361-375.
116. Monge A., Friesner R.A., Honig B. Proc. Natl. Acad. Sci. USA. 91:1994;5027-5029.
117. Monge M., Lathrop E., Gunn J.R., Shenkin P.S., Friesner R.D. J. Mol. Biol. 247:1995;995-1012.
118. Friesner R.A., Gunn J.R. Annu. Rev. Biophys. Biomol. Struct. 25:1996;315-342.
119. Dandekar T., Argos P. J. Mol. Biol. 256:1996;645-660.
120. Okamoto Y. Proteins. 19:1994;14-23.
121. Vieth M., Kolinski A., Skolnick J. Biochemistry. 35:1996;955-967.
122. D.B. Fogel, Evolutionary Computation: Towards a New Philosophy of Machine Intelligence, IEEE Press, New York, 1995.
123. Pedersen J.T., Moult J. Proteins. 23:1995;454-460.
124. McGarrah D.B., Judson R.S. J. Comp. Chem. 14:1993;1385-1395.
125. Dandekar T., Argos P. Protein Eng. 5:1992;637-645.
126. Pedersen J.T., Moult J. Curr. Op. Struct. Biol. 6:1996;227-231.
127. Clark D.E., Westhead D.R. J. Comp.-Aided Mol. Design. 10:1996;337-358.
128. Sun S., Thomas P.D., Dill K.A. Protein Eng. 8:1995;769-778.
129. LeGrand S.M., Merz K.M. Jr. Mol. Simulat. 13:1994;299-320.
130. Bowie J.U., Eisenberg D. Proc. Natl. Acad. Sci. USA. 91:1994;4436-4440.
131. Dandekar T., Leippe M. Folding and Design. 2:1997;47-52.
132. Saxena P., Whang I., Voziyanov Y., Harkey C., Argos P., Jayaram M., Dandekar T. Biochim. Biophys. Acta. 1340:1997;187-204.
133. Rabov A.A., Scheraga H.A. Protein Sci. 5:1996;1800-1815.
134. Tuffery P., Etchebest C., Hazout S., Lavery R. J. Biomol. Struct. Dyn. 8:1991;1267-1289.
135. Ring C.S., Cohen F.E. Isr. J. Chem. 34:1994;245-252.
136. Bouzida D., Kumar S., Swendson R.H. Phys. Rev. A 45:1992;8894-8901.
137. Harrison R.W. J. Comp. Chem. 14:1993;1112-1122.
138. Bruccoleri R.E., Karplus M. Biopolymers. 29:1990;1847-1862.
139. Smith P.E., van-Gunsteren W.F. J. Mol. Biol. 235:1994;629-636.
140. Clarage J.B., Romo T., Andrews B.K., Pettitt B.M., Phillips G.N. Jr. Proc. Natl. Acad. Sci. USA. 92:1995;3288-3292.
141. R. Elber, Curr. Op. Struct. Biol. 6 232-235.
142. Bassolino-Klimas D., Tejero R., Krystek S.R., Metzler W.J., Montelione G.T., Bruccoleri R.E. Protein Sci. 5:1996;593-603.
143. Dauber-Osguthorpe P., Maunder C.M., Osguthorpe D.J. J. Comput. Aided Mol. Des. 10:1996;177-185.
144. Karplus M., Sali A. Curr. Op. Struct. Biol. 5:1995;58-73.
145. Wilmanns M., Eisenberg D. Protein Eng. 8:1995;627-639.
146. Lichtarge O., Bourne H.R., Cohen F.E. J. Mol. Biol. 257:1996;342-358.
147. Crippen G.M. Easily searched protein folding potentials. J. Mol. Biol. 260:1996;467-475.
148. Elofsson A., Le-Grand S.M., Eisenberg D. Proteins. 23:1995;73-82.
149. Fraternali F., van-Gunsteren W.F. J. Mol. Biol. 256:1996;939-948.
150. Dinner A.R., Sali A., Karplus M. Proc. Natl. Acad. Sci. USA. 93:1996;8356-8361.
151. Unger R., Moult J. J. Mol. Biol. 259:1996;988-994.
152. Samudrala R., Pedersen J.T., Zhou H.B., Luo R., Fidelis K., Moult J. Proteins. 23:1995;327-336.
153. Bassolino-Klimas D., Tejero R., Krystek S.R., Metzler W.J., Montelione G.T., Bruccoleri R.E. Protein Sci. 5:1996;593-603.
154. Yue K., Dill K.A. Protein Sci. 5:1996;254-261.
155. Warwicker J. J.Mol. Biol. 236:1994;887-903.
156. Finkelstein A.V., Gutin A.M., Badretdinov A.Y. Proteins. 23:1995;151-162.
157. Ouzounis C., Bork P., Casari G., Sander C. Protein Sci. 4:1995;2424-2428.
158. Panchenko A.R., Luthey-Schulten Z., Wolynes P.G. Proc. Natl. Acad. Sci. USA. 93:1996;2008-2013.
159. Strynadka N.C., Eisenstein M., Katchalski-Katzir E., Shoichet B.K., Kuntz I.D., Abagyan R., Totrov M., Janin J., Cherfils J., Zimmerman F., Olson A., Duncan B., Rao M., Jackson R., Sternberg M., James M.N. Nature Structural Biology. 3:1996;209-210.
160. Unger R., Moult J. Bull. Math. Biol. 55:1994;1183-1198.