Structural basis of macromolecular recognition

Advances in Protein Chemistry

Volumn 61, Issue , 2002, Pages 9-73

  Wodak, Shoshana J ^a   Janin, Joël ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN;

CHEMICAL COMPOSITION; CHEMICAL STRUCTURE; CONFORMATIONAL TRANSITION; DISEASE CLASSIFICATION; ELECTRON MICROSCOPY; GEOMETRY; MACROMOLECULE; MATHEMATICAL COMPUTING; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN PROTEIN INTERACTION; REVIEW; SIMULATION; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS;

EID: 0036424666     PISSN: 00653233     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0065-3233(02)61001-0     Document Type: Review

References (171)

1. Ackermann, F., Herrmann, G., Posch, S., and Sagerer, G. (1998). Estimation and filtering of potential protein-protein docking positions. Bioinformatics 14(2), 196-205
2. Amadei, A., Linssen, A. B., and Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins 17(4), 412-425
3. Argos, P. (1988). An investigation of protein subunit and domain interfaces. Protein Eng. 2(2), 101-113
4. Bachar, O., Fischer, D., Nussinov, R., and Wolfson, H. (1993). A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Protein Eng. 6(3), 279-288
5. Beamer, L. J., and Pabo, C. O. (1992). Refined 1.8 Å crystal structure of the lambda repressor-operator complex. J. Mol. Biol. 227(1), 177-196
6. Berg, O. G., and von Hippel, P. H. (1985). Diffusion-controlled macromolecular interactions. Annu. Rev. Biophys. Biophys. Chem. 14, 131-160
7. Blom, N. S., and Sygusch, J. (1997). High resolution fast quantitative docking using Fourier domain correlation techniques. Proteins 27(4), 493-506
8. Bogan, A. A., and Thorn, K. S. (1998). Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280, 1-9
9. Braden, B. C., Fields, B. A., Ysern, X., Dall'Acqua, W., Goldbaum, F. A., Poljak, R. J., and Mariuzza, R. A. (1996). Crystal structure of an Fv-Fv idiotope-anti-idiotope complex at 1.9 Å resolution. J. Mol. Biol. 264, 137-151
10. Bryngelson, J. D., and Wolynes, P. G. (1987). Spin glasses and the statistical mechanics of protein folding. Proc. Natl. Acad. Sci. USA 84(21), 7524-7528
11. Buckle, A. M., Schreiber, G., and Fersht, A. R. (1994). Protein-protein recognition: Crystal structural analysis of a barnase-barstar complex at 2.0-Å resolution. Biochemistry 33(30), 8878-8889
12. Camacho, C. J., Kimura, S. R., DeLisi, C., and Vajda, S. (2000). Kinetics of desolvation-mediated protein-protein binding. Biophys. J. 78(3), 1094-1105
13. Camacho, C. J., Weng, Z., Vajda, S., and DeLisi, C. (1999). Free energy landscapes of encounter complexes in protein-protein association. Biophys. J. 76(3), 1166-1178
14. Carter, P. J., Winter, G., Wilkinson, A. J., and Fersht, A. R. (1984). The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus). Cell 38(3), 835-840
15. Carugo, O., and Argos, P. (1997). Protein-protein crystal-packing contacts. Protein Sci. 6(10), 2261-2263
16. Chen, R., and Weng, Z. (2002). Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 47, 281-294
17. Cherfils, J., Duquerroy, S., and Janin, J. (1991). Protein-protein recognition analyzed by docking simulation. Proteins 11(4), 271-280
18. Chitarra, V., Alzari, P. M., Bentley, G. A., Bhat, T. N., Eisele, J. L., Houdusse, A., Lescar, J., Souchon, H., and Poljak, R. J. (1993). Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex. Proc. Natl. Acad. Sci. USA 90(16), 7711-7715
19. Chothia, C., and Janin, J. (1975). Principles of protein-protein recognition. Nature 256(5520), 705-708
20. Clackson, T., and Wells, J. A. (1995). A hot spot of binding energy in a hormone-receptor interface. Science 267(5196), 383-386
21. Connolly, M. L. (1983). Analytical molecular surface calculation. J. Appl. Crystallogr. 16, 548-558
22. Connolly, M. L. (1985). Molecular surface triangulation. J. Appl. Crystallogr. 18, 499-505
23. Connolly, M. L. (1986). Shape complementarity at the hemoglobin alpha 1 beta 1 subunit interface. Biopolymers 25(7), 1229-1247
24. Dahiyat, B. I., and Mayo, S. L. (1997). De novo protein design: Fully automated sequence selection. Science 278(5335), 82-87
25. Dasgupta, S., lyer, G. H., Bryant, S. H., Lawrence, C. E., and Bell, J. A. (1997). Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins 28(4), 494-514
26. Davies, D. R., and Cohen, G. H. (1996). Interactions of protein antigens with antibodies. Proc. Natl. Acad. Sci. USA 93(1), 7-12
27. de Vos, A. M., Ultsch, M., and Kossiakoff, A. A. (1992). Human growth hormone and extracellular domain of its receptor: Crystal structure of the complex. Science 255(5042), 306-312
28. Dixon, J. S. (1997). Evaluation of the CASP2 docking section. Proteins Suppl. 1), 198-204
29. Elcock, A. H., Gabdoulline, R. R., Wade, R. C., and McCammon, J. A. (1999). Computer simulation of protein-protein association kinetics: Acetylcholinesterase-fasciculin. J. Mol. Biol. 291, 149-162
30. Elcock, A. H., Sept, D., and McCammon, J. A. (2001). Computer simulation of protein-protein interactions. J. Phys. Chem. B. 105(8), 1504-1518
31. Ermak, D. L., and McCammon, J. A. (1978). Brownian dynamics with hydrodynamic interactions. J. Chem. Phys. 69, 1352-1360
32. Finkelstein, A. V., and Janin, J. (1989). The price of lost freedom: Entropy of bimolecular complex formation. Protein Eng. 3(1), 1-3
33. Finney, J. L. (1975). Volume occupation, environment and accessibility in proteins: The problem of the protein surface. J. Mol. Biol. 96, 721-732
34. Fischer, D., Lin, S. L., Wolfson, H. L., and Nussinov, R. (1995a). A geometry-based suite of molecular docking processes. J. Mol. Biol. 248, 459-477
35. Fischer, D., Norel, R., Wolfson, H., and Nussinov, R. (1993). Surface motifs by a computer vision technique: Searches, detection, and implications for protein-ligand recognition. Proteins 16(3), 278-292
36. Fisher, H. F., and Singh, N. (1995). Calorimetric methods for interpreting protein-ligand interactions. Methods Enzymol. 259, 194-221
37. Fogolari, F., Elcock, A. H., Esposito, G., Viglino, P., Briggs, J. M., and McCammon, J. A. (1997). Electrostatic effects in homeodomain-DNA interactions. J. Mol. Biol. 267, 368-381
38. Ford, C. E., Skiba, N. P., Bae, H., Daaka, Y., Reuveny, E., Shekter, L. R., Rosal, R., Weng, G., Yang, C. S., and lyengar, R. (1998). Molecular basis for interactions of G protein beta-gamma subunits with effectors. Science 280(5367), 1271-1274
39. Frisch, C., Schreiber, G., Johnson, C. M., and Fersht, A. R. (1997). Thermodynamics of the interaction of barnase and barstar: Changes in free energy versus changes in enthalpy on mutation. J. Mol. Biol. 267, 696-706
40. Froloff, N., Windemuth, A., and Honig, B. (1997). On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions. Protein Sci. 6(6), 1293-1301
41. Fujinaga, M., Sielecki, A. R., Read, R. J., Ardelt, W., Laskowski, M., Jr., and James, M. N. (1987). Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 A resolution. J. Mol. Biol. 195, 397-418
42. Gabb, H. A., Jackson, R. M., and Sternberg, M. J. (1997). Modelling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol. 272, 106-120
43. Gabdoulline, R. R., and Wade, R. C. Effective charges for macromolecules in solvent. (1996). J. Phys. Chem. 100, 3868
44. Gabdoulline, R. R., and Wade, R. C. (1997). Simulation of the diffusional association of barnase and barstar. Biophys. J. 72(5), 1917-1929
45. Gabdoulline, R. R., and Wade, R. C. (1998). Brownian dynamics simulation of protein-protein diffusional encounter. Methods 14, 329-341
46. Gabdoulline, R. R., and Wade, R. C. (1999). On the protein-protein diffusional encounter complex. J. Mol. Recogn. 12(4), 226-234
47. Gamble, T. R., Vajdos, F. F., Yoo, S., Worthylake, D. K., Houseweart, M., Sundquist, W. I., and Hill, C. P. (1996). Crystal structure of human cyclophilin A bound to the aminoterminal domain of HIV-1 capsid. Cell 87(7), 1285-1294
48. Gardiner, E. J., Willett, P., and Artymiuk, P. J. (2001). Protein docking using a genetic algorithm. Proteins 44, 44-56
49. Gilson, M. K., and Honig, B. (1988). Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis. Proteins 4(1), 7-18
50. Gilson, M. K., Given, J. A., Bush, B. L., and McCammon, J. A. (1997). The statistical-thermodynamic basis for computation of binding affinities: A critical review. Biophys J. 72, 1047-1069
51. Goodsell, D. S., and Olson, A. J. (1993). Soluble proteins: Size, shape and function. Trends Biochem. Sci. 18(3), 65-68
52. Guillet, V., Lapthorn, A., and Mauguen, Y. (1993). Three-dimensional structure of a barnase-3′GMP complex at 2.2 Å resolution. FEBS Lett. 330(2), 137-140
53. Halperin, I., Ma, B., Wolfson, H., and Nissinov, R. (2002). Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 47, 409-443
54. Harpaz, Y., Gerstein, M., and Chothia, C. (1994). Volume changes on protein folding. Structure 2(7), 641-649
55. Harrison, R. W., Kourinov, I. V., and Andrews, L. C. (1994). The Fourier-Green's function and the rapid evaluation of molecular potentials. Protein Eng. 7(3), 359-369
56. Hartley, R. W. (1993). Directed mutagenesis and barnase-barstar recognition. Biochemistry 32(23), 5978-5984
57. Hegde, R. S., Grossman, S. R., Laimins, L. A., and Sigler, P. B. (1992). Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature 359(6395), 505-512
58. Hendsch, Z. S., and Tidor, B. (1999). Electrostatic interactions in the GCN4 leucine zipper: Substantial contributions arise from intramolecular interactions enhanced on binding. Protein Sci. 8(7), 1381-1392
59. Hibbits, K. A., Gill, D. S., and Willson, R. C. (1994). Isothermal titration calorimetric study of the association of hen egg lysozyme and the anti-lysozyme antibody HyHEL-5. Biochemistry 33(12), 3584-3590
60. Hilvert, D. (2000). Genetic selection as a tool in mechanistic enzymology and protein design. Ernst Schering Res. Found. Workshop(32), 253-268
61. Honig, B., and Nicholls, A. (1995), Classical electrostatics in biology and chemistry. Science 268(5214), 1144-1149
62. Horovitz, A. (1987). Non-additivity in protein-protein interactions. J. Mol. Biol. 196, 733-735
63. Housset, D., Mazza, G., Gregoire, C., Piras, C., Malissen, B., and Fontecilla-Camps, J. C. (1997). The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain. EMBO J. 16(14), 4205-4216
64. Huber, R., Kukla, D., Bode, W., Schwager, P., Bartels, K., Deisenhofer, J., and Steigemann, W. (1974). Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 Å resolution. J. Mol. Biol. 89, 73-101
65. Janin, J. (1995). Elusive affinities. Proteins 21(1), 30-39
66. Janin, J. (1996). Quantifying biological specificity: The statistical mechanics of molecular recognition. Proteins 25(4), 438-445
67. Janin, J. (1997). Elusive affinities, Proteins 21, 30-39
68. Janin, J., and Chothia, C, (1976). Stability and specificity of protein-protein interactions: The case of the trypsin-trypsin inhibitor complexes. J. Mol. Biol. 100, 197-211
69. Janin, J., and Chothia, C. (1990). The structure of protein-protein recognition sites. J. Biol. Chem. 265(27), 16027-16030
70. Janin, J., Miller, S., and Chothia, C. (1988). Surface, subunit interfaces and interior of oligomeric proteins. J. Mol. Biol. 204, 155-164
71. Janin, J., and Rodier, F. (1995). Protein-protein interaction at crystal contacts. Proteins 23(4), 580-587
72. Janin, J., and Wodak, S. J. (1985). Reaction pathway for the quaternary structure change in hemoglobin. Biopolymers 24(3), 509-526
73. Jiang, F., and Kim, S. H. (1991). "Soft docking": Matching of molecular surface cubes. J. Mol. Biol. 219, 79-102
74. Jones, S., and Thornton, J. M. (1995). Protein-protein interactions: A review of protein dimer structures. Prog. Biophys. Mol. Biol. 63(1), 31-65
75. Jones, S., and Thornton, J. M. (1996). Principles of protein-protein interactions. Proc. Natl. Acad. Sci. USA 93(1), 13-20
76. Jones, S., van Heyningen, P., Berman, H. M., and Thornton, J. M. (1999). Protein-DNA interactions: A structural analysis. J. Mol. Biol. 287, 877-896
77. Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A. A., Aflalo, C., and Vakser, I. A. (1992). Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. USA 89(6), 2195-2199
78. Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., and Ferrin, T. E. (1982). A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161, 269-288
79. Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J., and Hendrickson, W. A. (1998). Structure of an HIV gpl20 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 393(6686), 648-659
80. Ladbury, J. E., and Chowdhry, B. Z. (1996). Sensing the heat: The application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions. Chem. Biol. 3(10), 791-801
81. Ladbury, J. E., Wright, J. G., Sturtevant, J. M., and Sigler, P. B. (1994). A thermodynamic study of the trp repressor-operator interaction. J. Mol. Biol. 238, 669-681
82. Lambright, D. G., Noel, J. P., Hamm, H. E., and Sigler, P. B. (1994). Structural determinants for activation of the alpha-subunit of a heterotrimeric G protein. Nature 369(6482), 621-628
83. Lambright, D. G., Sondek, J., Bohm, A., Skiba, N. P., Hamm, H. E., and Sigler, P. B. (1996). The 2.0 Å crystal structure of a heterotrimeric G protein. Nature 379(6563), 311-319
84. Larsen, T. A., Olson, A. J., and Goodsell, D. S. (1998). Morphology of protein-protein interfaces. Structure 6(4), 421-427
85. Laskowski, R. A. (1995). SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph. 13(5), 323-330
86. Lawrence, M. C., and Colman, P. M. (1993). Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946-950
87. Lee, B., and Richards, F. M. (1971). The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 55, 379-400
88. Lee, R. H., and Rose, G. D. (1985). Molecular recognition. I. Automatic identification of topographic surface features. Biopolymers 24(8), 1613-1627
89. Levitt, M. (1976). A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104, 59-107
90. Lin, S. L., Nussinov, R., Fischer, D., and Wolfson, H. J. (1994). Molecular surface representations by sparse critical points. Proteins 18(1), 94-101
91. Lo Conte, L. L., Chothia, C., and Janin, J. (1999). The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285, 2177-2198
92. Madura, J. D., Briggs, J. M., Wade, R. C., Davis, M. E., Luty, B. A., Ilin, A., Antosiewicz, J., Gilson, M. K., Bagheri, B., and Scott, L. R. (1995). Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian dynamics program. Comp. Phys. Commun. 91, 57-95
93. Madura, J. D., Briggs, J. M., Wade, R. C., and Gabdoulline, R. R. (1998). Brownian dynamics. In "Encyclopedia of Computational Chemistry" (P. V. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Schreiner, and H. F. Schaefer, eds.), vol. 1, pp. 141-154. John Wiley and Sons, UK
94. Madura, J. D., Davis, M. E., Gilson, M. K., Wade, R. C., Luty, B. A., and McCammon, J. A. (1994). Biological applications of electrostatic calculations and Brownian dynamics simulations. Comp. Chem. Rev. 5, 229-267
95. Makhatadze, G. I., and Privalov, P. L. (1996). On the entropy of protein folding. Protein Sci. 5(3), 507-510
96. Marquart, M., Walter, J., Deisenhofer, J., Bode, W., and Huber, R. (1983). The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crystallogr. Sect. B. 39, 480-490
97. Mauguen, Y., Hartley, R. W., Dodson, E.J., Dodson, G. G., Bricogne, G., Chothia, C., and Jack, A. (1982). Molecular structure of a new family of ribonucleases. Nature 297(5862), 162-164
98. McDonald, I. K., and Thornton, J. M. (1994). Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238, 777-793
99. Meyer, M., Wilson, P., and Schomburg, D. (1996). Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking. J. Mol. Biol. 264, 199-210
100. Miller, S., Lesk, A. M., Janin, J., and Chothia, C. (1987). The accessible surface area and stability of oligomeric proteins. Nature 328(6133), 834-836
101. Misra, V. K., Hecht, J. L., Sharp, K. A., Friedman, R. A., and Honig, B. (1994a). Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease. J. Mol. Biol. 238, 264-280
102. Misra, V. K., Sharp, K. A., Friedman, R. A., and Honig, B. (1994b). Salt effects on ligand-DNA binding. Minor groove binding antibiotics. J. Mol. Biol. 238, 245-263
103. Misra, V. K., Hecht, J. L., Yang, A. S., and Honig, B. (1998). Electrostatic contributions to the binding free energy of the lambdacI repressor to DNA, Biophys. J. 75(5), 2262-2273
104. Nadassy, K., Tomas-Oliveira, I., Alberts, I., Janin, J., and Wodak, S. J. (2001). Standard atomic volumes in double-stranded DNA and packing in protein-DNA interfaces. Nucleic Acids Res. 29(16), 3362-3376
105. Nadassy, K., Wodak, S. J., and Janin, J. (1999). Structural features of protein-nucleic acid recognition sites. Biochemistry 38(7), 1999-2017
106. Nikolov, D. B., and Burley, S. K. (1994). 2.1 Å resolution refined structure of a TATA box-binding protein (TBP). Nat. Struct. Biol. 1(9), 621-637
107. Nikolov, D. B., Chen, H., Halay, E. D., Hoffman, A., Roeder, R. G., and Burley, S. K. (1996). Crystal structure of a human TATA box-binding protein/TATA element complex. Proc. Natl. Acad. Sci. USA 93(10), 4862-4867
108. Noel, J. P., Hamm, H. E., and Sigler, P. B. (1993). The 2.2 Å crystal structure of transducin-alpha complexed with GTP gamma S. Nature 366(6456), 654-663
109. Norel, R., Fischer, D., Wolfson, H. J., and Nussinov, R. (1994). Molecular surface recognition by a computer vision-based technique. Protein Eng. 7(1), 39-46
110. Northrup, S. H., and Erickson, H. P. (1992). Kinetics of protein-protein association explained by Brownian dynamics computer simulation. Proc. Natl. Acad. Sci. USA 89(8), 3338-3342
111. Northrup, S. H., Boles, J. O., and Reynolds, J. C. (1988). Brownian dynamics of cytochrome c and cytochrome c peroxidase association. Science 241, 372-384
112. Ogata, K., and Wodak, S. J. Conserved Water Molecules in MHC Class-I Molecules and Their Putative Structural and Functional Roles. Submitted for publication
113. Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G., and Steitz, T. A. (1985a). Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature 313(6005), 762-766
114. Ollis, D. L., Kline, C., and Steitz, T. A. (1985b). Domain of E. coli DNA polymerase I showing sequence homology to T7 DNA polymerase. Nature 313(6005), 818-819
115. Oobatake, M., and Ooi, T (1993). Hydration and heat stability effects on protein unfolding. Prog. Biophys. Mol. Biol. 59(3), 237-284
116. Palma, P. N., Krippahl, L., Wampler, J. E., and Moura, J. J. (2000). BIGGER: A new (soft) docking algorithm for predicting protein interactions. Proteins 39, 44-56
117. Pelletier, H., and Kraut, J. (1992). Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c. Science 258(5089), 1748-1755
118. Phizicky, E. M., and Fields, S. (1995). Protein-protein interactions: Methods for detection and analysis. Microbiol. Rev. 59(1), 94-123
119. Press, W. H., Teukolsky, S. A., Vetterling, W. T., and Flannery, B. P. (1992). "Numerical Recipes in C," 2nd Ed. Cambridge Univ. Press, Cambridge
120. Privalov, P. L., and Gill, S. J. (1988). Stability of protein structure and hydrophobic interaction. Adv. Protein Chem. 39, 191-234
121. Radic, Z., Kirchhoff, P. D., Quinn, D. M., McCammon, J. A., and Taylor, P. (1997). Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin. J. Biol. Chem. 272(37), 23265-23277
122. Ravichandran, S., and Talbot, J. (2000). Mobility of adsorbed proteins: A Brownian dynamics study. Biophys. J. 78(1), 110-120
123. Reddy, V. S., Giesing, H. A., Morton, R. T., Kumar, A., Post, C. B., Brooks, C. L., III, and Johnson, J. E. (1998). Energetics of quasiequivalence: Computational analysis of protein-protein interactions in icosahedral viruses. Biophys. J. 74(1), 546-558
124. Richards, F. M. (1974). The interpretation of protein structures: Total volume, group volume distributions and packing density. J. Mol. Biol. 82, 1-14
125. Ritchie, D. W., and Kemp, G. J. (2000). Protein docking using spherical polar Fourier correlations. Proteins 39(2), 178-194
126. Rydel, T. J., Tulinsky, A., Bode, W., and Huber, R. (1991). Refined structure of the hirudinthrombin complex. J. Mol. Biol. 221, 583-601
127. Schapira, M., Totrov, M., and Abagyan, R. (1999). Prediction of the binding energy for small molecules, peptides and proteins. J. Mol. Recogn. 12(3), 177-190
128. Schreiber, G., and Fersht, A. R. (1993). The refolding of cis- and trans-peptidylprolyl isomers of barstar. Biochemistry 32(41), 11195-11203
129. Schreiber, G., and Fersht, A. R. (1995). Energetics of protein-protein interactions: Analysis of the barnase-barstar interface by single mutations and double mutant cycles. J. Mol. Biol. 248, 478-486
130. Schreiber, G., and Fersht, A. R. (1996). Rapid, electrostatically assisted association of proteins. Nat. Struct. Biol. 3 (5), 427-431
131. Schwehm, J. M., and Stites, W. E. (1998). Application of automated methods for determination of protein conformational stability. Methods Enzymol. 295, 150-170
132. Seizer, T., Albeck, S., and Schreiber, G. (2000). Rational design of faster associating and tighter binding protein complexes. Nat. Struct. Biol. 7(7), 537-541
133. Sept, D., Elcock, A. H., and McCammon, J. A. (1999). Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry. J. Mol. Biol. 294, 1181-1189
134. Shakked, Z., Guzikevich-Guerstein, G., Frolow, F., Rabinovich, D., Joachimiak, A., and Sigler, P. B. (1994). Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature 368(6470), 469-473
135. Sheinerman, F. B., Norel, R., and Honig, B. (2000). Electrostatic aspects of protein-protein interactions. Curr. Opin. Struct. Biol. 10(2), 153-159
136. Sheriff, S., Silverton, E. W., Padlan, E. A., Cohen, G. H., Smith-Gill, S. J., Finzel, B. C., and Davies, D. R. (1987). Three-dimensional structure of an antibody-antigen complex. Proc. Natl. Acad. Sci. USA 84(22), 8075-8079
137. Shoemaker, B. A., Portman, J. J., and Wolynes, P. G. (2000). Speeding molecular recognition by using the folding funnel: The fly-casting mechanism. Proc. Natl. Acad. Sci. USA 97(16), 8868-8873
138. Shoichet, B. K., Bodian, D. L., and Kuntz, I. D. (1992). Molecular docking using shape descriptors. J. Comput. Chem. 13(3), 380-397
139. Shoichet, B. K., and Kuntz, I. D. (1991). Protein docking and complementarity. J. Mol. Biol. 221, 327-346
140. Smith, G. R., and Sternberg, M. J. (2002). Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 12, 28-35
141. Smoluchowski, M. V. (1917). Versuch einer mathematischen Theorie der KoagulationsKinetik KolloiderLoeschungen. J. Phys. Chem. 92, 129-168
142. Sondek, J., Bohm, A., Lambright, D. G., Hamm, H. E., and Sigler, P. B. (1996). Crystal structure of a G-protein beta gamma dimer at 2.1 Å resolution. Nature 379(6563), 369-374
143. Srere, P. A. (1999). Protein interactions. Methods 19(2), 193
144. Strynadka, N. C., Eisenstein, M., Katchalski-Katzir, E., Shoichet, B. K., Kuntz, I. D., Abagyan, R., Totrov, M., Janin, J., Cherfils, J., and Zimmerman, F. (1996). Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat. Struct. Biol. 3(3), 233-239
145. Thorn, K. S., and Bogan, A. A. (2001). ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 17(3), 284-285
146. Tovchigrechko, A., Wells, C. A., and Vakser, I. (2001). Docking of Protein Models. In press
147. Tsai, J., Taylor, R., Chothia, C., and Gerstein, M. (1999). The packing density in proteins: Standard radii and volumes. J. Mol. Biol. 290, 253-266
148. Vakser, I. A. (1995). Protein docking for low-resolution structures. Protein Eng. 8(4), 371-377
149. Vakser, I. A. (1996). Long-distance potentials: An approach to the multiple-minima problem in ligand-receptor interaction. Protein Eng. 9(1), 37-41
150. Vakser, I. A. (1997). Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins Suppl. 1), 226-230
151. Vakser, I. A., and Aflalo, C. (1994). Hydrophobic docking: A proposed enhancement to molecular recognition techniques. Proteins 20(4), 320-329
152. van de Locht, A., Stubbs, M. T., Bode, W., Friedrich, T., Bollschweiler, C., Hoffken, W., and Huber, R. (1996). The ornithodorin-thrombin crystal structure, a key to the TAP enigma? EMBO J. 15(22), 6011-6017
153. Vincent, J. P., and Lazdunski, M. (1972). Trypsin-pancreatic trypsin inhibitor association. Dynamics of the interaction and role of disulfide bridges. Biochemistry 11(16), 2967-2977
154. Vitkup, D., Melamud, E., Moult, J., and Sander, C. (2001). Completeness in structural genomics. Nat. Struct. Biol. 8(6), 559-566
155. von Hippel, P. H., and Berg, O. G. (1989). Facilitated target location in biological systems. J. Biol. Chem. 264(2), 675-678
156. Wade, R. C. (1996). Brownian dynamics simulations of enzyme-substrate encounter. Biochem. Soc. Trans. 24(1), 254-259
157. Wang, H. (1991). Grid-search molecular accessible surface algorithm for solving the protein docking problem. J. Comp. Chem. 12, 746-750
158. Wang, J. H., Smolyar, A., Tan, K., Liu, J. H., Kim, M., Sun, Z. Y., Wagner, G., and Reinherz, E. L. (1999). Structure of a heterophilic adhesion complex between the human CD2 and CD58 (LFA-3) counterreceptors. Cell 97(6), 791-803
159. Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta Jr., S., and Weiner, P. (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784
160. Welch, M., Chinardet, N., Mourey, L., Birck, C., and Samama, J. P. (1998). Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY. Nat. Struct. Biol. 5(1), 25-29
161. Werner, M. H., and Burley, S. K. (1997). Architectural transcription factors: Proteins that remodel DNA. Cell 88(6), 733-736
162. Wernisch, L., Hery, S., and Wodak, S. J. (2000). Automatic protein design with all atom force-fields by exact and heuristic optimization. J. Mol. Biol. 301, 713-736
163. Wodak, S. J., and Janin, J. (1978). Computer analysis of protein-protein interaction. J. Mol. Biol. 124, 323-342
164. Wodak, S. J., and Janin, J. (1980). Analytical approximation to the accessible surface area of proteins. Proc. Natl. Acad. Sci USA. 77(4), 1736-1740
165. Wriggers, W., Milligan, R. A., and McCammon, J. A. (1999). Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 125, 185-195
166. Xenarios, I., Rice, D. W., Salwinski, L., Baron, M. K., Marcotte, E. M., and Eisenberg, D. (2000). DIP: The database of interacting proteins. Nucleic Acids Res. 28(1), 289-291
167. Xiao, L., and Honig, B. (1999). Electrostatic contributions to the stability of hyperthermophilic proteins. J. Mol. Biol. 289, 1435-1444
168. Xu, D., Tsai, C. J., and Nussinov, R. (1997). Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Eng. 10(9), 999-1012
169. Ysern, X., Li, H., and Mariuzza, R. A. (1998). Imperfect interfaces. Nat. Struct. Biol. 5(6), 412-414
170. Zachmann, C. D., Heiden, W., Schlenkrich, M., and Brickmann, J. (1992). Topological analysis of complex molecular surfaces. J. Comp. Chem. 13(1), 76-84
171. Zhang, C., Vasmatzis, G., Cornette, J. L., and DeLisi, C. (1997). Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol. 267, 707-726