Crossref journal-article
American Association for the Advancement of Science (AAAS)
Science (221)
Abstract

The prediction of the structures and interactions of biological macromolecules at the atomic level and the design of new structures and interactions are critical tests of our understanding of the interatomic interactions that underlie molecular biology. Equally important, the capability to accurately predict and design macromolecular structures and interactions would streamline the interpretation of genome sequence information and allow the creation of macromolecules with new and useful functions. This review summarizes recent progress in modeling that suggests that we are entering an era in which high-resolution prediction and design will make increasingly important contributions to biology and medicine.

Bibliography

Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., & Baker, D. (2005). Progress in Modeling of Protein Structures and Interactions. Science, 310(5748), 638–642.

Authors 5
  1. Ora Schueler-Furman (first)
  2. Chu Wang (additional)
  3. Phil Bradley (additional)
  4. Kira Misura (additional)
  5. David Baker (additional)
References 71 Referenced 239
  1. 10.1126/science.181.4096.223
  2. R. Schleif, Methods Enzymol.383, 28 (2004). (10.1016/S0076-6879(04)83002-7) / Methods Enzymol. (2004)
  3. M. Karplus, J. A. McCammon, Nat. Struct. Biol.9, 646 (2002). (10.1038/nsb0902-646) / Nat. Struct. Biol. (2002)
  4. J. Moult, Curr. Opin. Struct. Biol.15, 285 (2005). (10.1016/j.sbi.2005.05.011) / Curr. Opin. Struct. Biol. (2005)
  5. J. Janin, Protein Sci.14, 278 (2005). (10.1110/ps.041081905) / Protein Sci. (2005)
  6. J. Janin et al., Proteins52, 2 (2003). (10.1002/prot.10381) / Proteins (2003)
  7. C. A. Rohl, C. E. Strauss, K. M. Misura, D. Baker, Methods Enzymol.383, 66 (2004). (10.1016/S0076-6879(04)83004-0) / Methods Enzymol. (2004)
  8. K. A. Bava, M. M. Gromiha, H. Uedaira, K. Kitajima, A. Sarai, Nucleic Acids Res.32, D120 (2004). (10.1093/nar/gkh082) / Nucleic Acids Res. (2004)
  9. B. W. Matthews, Adv. Protein Chem.46, 249 (1995). (10.1016/S0065-3233(08)60337-X) / Adv. Protein Chem. (1995)
  10. 10.1126/science.2315699
  11. J. T. Kellis Jr., K. Nyberg, D. Sali, A. R. Fersht, Nature333, 784 (1988). (10.1038/333784a0) / Nature (1988)
  12. 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N
  13. M. Feig, C. L. Brooks III, Curr. Opin. Struct. Biol.14, 217 (2004). (10.1016/j.sbi.2004.03.009) / Curr. Opin. Struct. Biol. (2004)
  14. A. D. Mackerell Jr., J. Comput. Chem.25, 1584 (2004). (10.1002/jcc.20082) / J. Comput. Chem. (2004)
  15. B. Brooks et al., J. Comput. Chem.4, 187 (1983). (10.1002/jcc.540040211) / J. Comput. Chem. (1983)
  16. W. Cornell et al., J. Am. Chem. Soc.117, 5179 (1995). (10.1021/ja00124a002) / J. Am. Chem. Soc. (1995)
  17. D. B. Gordon, S. A. Marshall, S. L. Mayo, Curr. Opin. Struct. Biol.9, 509 (1999). (10.1016/S0959-440X(99)80072-4) / Curr. Opin. Struct. Biol. (1999)
  18. A. V. Morozov, T. Kortemme, K. Tsemekhman, D. Baker, Proc. Natl. Acad. Sci. U.S.A.101, 6946 (2004). (10.1073/pnas.0307578101) / Proc. Natl. Acad. Sci. U.S.A. (2004)
  19. C. Levinthal, in Mossbauer Spectroscopy in Biological Systems: Proceedings of a Meeting Held at Allerton House, Monticello, Illinois, J. T. P. DeBrunner, E. Munck, Eds. (Univ. of Illinois Press, Urbana, 1969), pp. 22–24. / Mossbauer Spectroscopy in Biological Systems: Proceedings of a Meeting Held at Allerton House, Monticello, Illinois (1969)
  20. U. H. Hansmann, Y. Okamoto, Curr. Opin. Struct. Biol.9, 177 (1999). (10.1016/S0959-440X(99)80025-6) / Curr. Opin. Struct. Biol. (1999)
  21. K. Tai, Biophys. Chem.107, 213 (2004). (10.1016/j.bpc.2003.09.010) / Biophys. Chem. (2004)
  22. M. P. Jacobson et al., Proteins55, 351 (2004). (10.1002/prot.10613) / Proteins (2004)
  23. Z. Li, H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A.84, 6611 (1987). (10.1073/pnas.84.19.6611) / Proc. Natl. Acad. Sci. U.S.A. (1987)
  24. R. Abagyan, M. Totrov, J. Mol. Biol.235, 983 (1994). (10.1006/jmbi.1994.1052) / J. Mol. Biol. (1994)
  25. E. Katchalski-Katzir et al., Proc. Natl. Acad. Sci. U.S.A.89, 2195 (1992). (10.1073/pnas.89.6.2195) / Proc. Natl. Acad. Sci. U.S.A. (1992)
  26. R. Mendez, R. Leplae, M. F. Lensink, S. J. Wodak, Proteins60, 150 (2005). (10.1002/prot.20551) / Proteins (2005)
  27. 10.1021/ja026939x
  28. J. U. Bowie, D. Eisenberg, Proc. Natl. Acad. Sci. U.S.A.91, 4436 (1994). (10.1073/pnas.91.10.4436) / Proc. Natl. Acad. Sci. U.S.A. (1994)
  29. B. Park, M. Levitt, J. Mol. Biol.258, 367 (1996). (10.1006/jmbi.1996.0256) / J. Mol. Biol. (1996)
  30. D. T. Jones, L. J. McGuffin, Proteins53 (suppl. 6), 480 (2003). (10.1002/prot.10542) / Proteins (2003)
  31. J. Skolnick et al., Proteins53 (suppl. 6), 469 (2003). (10.1002/prot.10551) / Proteins (2003)
  32. Q. Fang, D. Shortle, Proteins53 (suppl. 6), 486 (2003). (10.1002/prot.10541) / Proteins (2003)
  33. K. T. Simons, C. Kooperberg, E. Huang, D. Baker, J. Mol. Biol.268, 209 (1997). (10.1006/jmbi.1997.0959) / J. Mol. Biol. (1997)
  34. 10.1126/science.1113801
  35. 10.1016/0022-2836(87)90358-5
  36. 10.1126/science.278.5335.82
  37. 10.1126/science.282.5393.1462
  38. 10.1016/j.cbpa.2003.12.008
  39. 10.1016/S1097-2765(02)00690-1
  40. 10.1038/nsmb749
  41. 10.1016/S0022-2836(02)00881-1
  42. 10.1126/science.1089427
  43. M. von Grotthuss, L. S. Wyrwicz, J. Pas, L. Rychlewski, Science304, 1597 (2004). / Science (2004)
  44. 10.1038/nature01556
  45. 10.1073/pnas.251555398
  46. 10.1073/pnas.0404387101
  47. 10.1126/science.1098432
  48. G. E. Moore, Electronics38, 114 (1965). / Electronics (1965)
  49. 10.1016/j.sbi.2004.01.009
  50. S. Y. Chung, S. Subbiah, Pac. Symp. Biocomput.,126 (1996). / Pac. Symp. Biocomput., (1996)
  51. M. Schlosshauer, D. Baker, Protein Sci.13, 1660 (2004). (10.1110/ps.03517304) / Protein Sci. (2004)
  52. J. D. Bryngelson, J. N. Onuchic, N. D. Socci, P. G. Wolynes, Proteins21, 167 (1995). (10.1002/prot.340210302) / Proteins (1995)
  53. The similarity of predictions and designs with crystal structures is not likely to be an artifact of the use of force fields in structure determination: X-ray structure determination at high resolution is almost entirely driven by experimental diffraction data and the force fields typically used in refinement differ from those used in the prediction and design calculations.
  54. 10.1006/jmbi.1995.0396
  55. E. Eyal, S. Gerzon, V. Potapov, M. Edelman, V. Sobolev, J. Mol. Biol.351, 431 (2005). (10.1016/j.jmb.2005.05.066) / J. Mol. Biol. (2005)
  56. T. S. Ulmer, B. E. Ramirez, F. Delaglio, A. Bax, J. Am. Chem. Soc.125, 9179 (2003). (10.1021/ja0350684) / J. Am. Chem. Soc. (2003)
  57. 10.1016/S0065-3233(03)66002-X
  58. A. Tramontano, V. Morea, Proteins53 (suppl. 6), 352 (2003). (10.1002/prot.10543) / Proteins (2003)
  59. G. Wang, R. L. Dunbrack Jr., Protein Sci.13, 1612 (2004). (10.1110/ps.03601504) / Protein Sci. (2004)
  60. K. Ginalski CASP6 Abstract Book (http://predictioncenter.org/casp6/abstracts/abstract.html) 64 (2004).
  61. A. Fiser, A. Sali, Methods Enzymol.374, 461 (2003). (10.1016/S0076-6879(03)74020-8) / Methods Enzymol. (2003)
  62. 10.1093/nar/25.17.3389
  63. D. T. Jones, J. Mol. Biol.292, 195 (1999). (10.1006/jmbi.1999.3091) / J. Mol. Biol. (1999)
  64. A. A. Canutescu, A. A. Shelenkov, R. L. Dunbrack Jr., Protein Sci.12, 2001 (2003). (10.1110/ps.03154503) / Protein Sci. (2003)
  65. D. Eisenberg, R. Luthy, J. U. Bowie, Methods Enzymol.277, 396 (1997). (10.1016/S0076-6879(97)77022-8) / Methods Enzymol. (1997)
  66. A. L. Carvalho et al., Proc. Natl. Acad. Sci. U.S.A.100, 13809 (2003). (10.1073/pnas.1936124100) / Proc. Natl. Acad. Sci. U.S.A. (2003)
  67. 10.1093/emboj/17.24.7505
  68. M. Graille, L. Mora, R. H. Buckingham, H. Van Tilbeurgh, M. De Zamaroczy, EMBO J.23, 1474 (2004). (10.1038/sj.emboj.7600162) / EMBO J. (2004)
  69. M. Kanagawa S. Yokoyama S. Kuramitsu unpublished data.
  70. O. Schueler-Furman, C. Wang, D. Baker, Proteins60, 187 (2005). (10.1002/prot.20556) / Proteins (2005)
  71. The software used in the prediction and design examples described above is available free for academic use in the ROSETTA software package (http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/Rosetta/) and personal computers can be enlisted in the conformational sampling essential to the prediction effort at http://boinc.bakerlab.org/rosetta/.
Dates
Type When
Created 19 years, 10 months ago (Oct. 27, 2005, 6:38 p.m.)
Deposited 1 year, 7 months ago (Jan. 9, 2024, 8:53 p.m.)
Indexed 3 months, 3 weeks ago (May 15, 2025, 12:11 a.m.)
Issued 19 years, 10 months ago (Oct. 28, 2005)
Published 19 years, 10 months ago (Oct. 28, 2005)
Published Print 19 years, 10 months ago (Oct. 28, 2005)
Funders 0

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@article{Schueler_Furman_2005, title={Progress in Modeling of Protein Structures and Interactions}, volume={310}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.1112160}, DOI={10.1126/science.1112160}, number={5748}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Schueler-Furman, Ora and Wang, Chu and Bradley, Phil and Misura, Kira and Baker, David}, year={2005}, month=oct, pages={638–642} }