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SnB References

  • A. The minimal function
    1. Debaerdemaeker, T. & Woolfson, M.M. (1983). On the application of phase relationships to complex structures XXII. Techniques for random phase refinement, Acta Cryst. A39, 193-196. [pdf]
    2. Hauptman, H.A. (1991). A minimal principle in the phase problem. In Crystallographic Computing 5: from Chemistry to Biology, edited by D.Moras, A.D. Podjarny & J.C. Thierry, 324-332. Oxford: IUCr & Oxford University Press. [pdf]
    3. DeTitta, G.T., Weeks, C.M., Thuman, P., Miller, R. & Hauptman, H.A. (1994). Structure solution by minimal function phase refinement and Fourier filtering: theoretical basis, Acta Cryst. A50, 203-210. [pdf]
  • B. The Shake-and-Bake (dual-space) phasing method
    1. Weeks, C.M., DeTitta, G.T., Miller, R. & Hauptman, H.A. (1993). Applications of the minimal principle to peptide structures, Acta Cryst. D49, 179-181. [pdf]
    2. Weeks, C.M., DeTitta, G.T., Hauptman, H.A., Thuman, P. & Miller, R. (1994). Structure solution by minimal function phase refinement and Fourier filtering: II. implementation and applications, Acta Cryst. A50, 210-220. [pdf]
    3. Xu, H., Weeks, C.M., Deacon, A.M., Miller, R. & Hauptman, H.A. (2000). Ill-conditioned Shake-and-Bake: The trap of the false minimum, Acta Cryst. A56, 112-118. [pdf]
    4. Xu, H., Hauptman, H.A. & Weeks, C.M. & Miller, R. (2000). P1 Shake-and-Bake:  can success be guaranteed?  Acta Cryst. D56, 238-240. [PubMed]
    5. Weeks, C.M., Sheldrick, G.M., Miller, R., Uson, I. & Hauptman, H.A. (2001). Ab initio phasing by dual-space direct methods. In the proceedings of the 18th European Crystallographic Association Meeting: Advances in Structure Analysis, R. Kužel, J. Hašek (Eds.), Czech & Slovak Cryst. Assn. Prague, pp. 37-64. [pdf]
    6. Sheldrick, G.M., Hauptman, H.A., Weeks, C.M., Miller, R. & Usón, I.  (2001). Chapter 16.1, Ab initio phasing.  In  International Tables of Macromolecular Crystallography, Vol. F, M.G. Rossman & E. Arnold (Eds.), Kluwer Academic Publishers, Dordrecht, pp. 333-351.
    7. Xu, H. & Hauptman, H. A. (2004). Statistical approach to the phase problem.  Acta Cryst. A60, 153-157. [PubMed]
  • C. SnB program
    1. Version 1.5: Miller, R., Gallo, S.M., Khalak, H.G. & Weeks, C.M. (1994). SnB: crystal structure determination via Shake-and-Bake, J. Appl. Cryst. 27, 613-621. [pdf]
    2. Version 2.0: Weeks, C.M. & Miller, R. (1999). The design and implementation of SnB v2.0, J. Appl. Cryst. 32, 120-124. [pdf]
    3. Rappleye, J., Innus, M., Weeks, C.M. & Miller, R. (2002). SnB version 2.2:  an example of crystallographic multiprocessing.  J. Appl. Cryst. 35, 374-376. [URL link]
    4. Miller, R., Shah, N., Green, M. L., Furey, W. & Weeks, C. M. (2007). Shake-and-Bake on the grid, J. Appl. Cryst. 40, 938-944. [URL link]
  • D. Significant Shake-and-Bake applications
    1. First unknown: Miller, R., DeTitta, G.T., Jones, R., Langs, D.A., Weeks, C.M. & Hauptman, H.A. (1993). On the application of the minimal principle to solve unknown structures, Science 259, 1430-1433. [pdf]
    2. First large molecule: Weeks, C.M., Hauptman, H.A., Smith, G.D., Blessing, R.H., Teeter, M.M. & Miller, R. (1995). Crambin: A direct solution for a 400 atom structure, Acta Cryst. D51, 33-38. [pdf]
    3. First substructure: Smith, G.D., Nagar, B., Rini, J.M., Hauptman, H.A. & Blessing, R.H. (1998). The use of SnB to determine an anomalous scattering substructure, Acta Cryst. D54, 799-804. [pdf]
    4. First unknown substructure: Turner, M.A., Yuan, C.-S., Borchardt, R.T., Hershfield, M.S., Smith, G.D. & Howell, P.L. (1998). Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength, Nature Structural Biology 5, 369-376. [pdf]
    5. Large P1 structure: Deacon, A.M., Weeks, C.M., Miller, R. & Ealick, S.E. (1998). The Shake-and-Bake structure determination of triclinic lysozyme.  Proc. Natl. Acad. Sci. USA, 95, 9284-9289. [PubMed]
  • E. SnB parameters
    1. Chang, C.-S., Weeks, C.M., Miller, R. & Hauptman, H.A. (1997). Incorporating tangent refinement in the Shake-and-Bake formalism, Acta Cryst. A53, 436-444. [pdf]
    2. Weeks, C. M. & Miller, R. (1999). Optimizing Shake-and-Bake for proteins, Acta Cryst. D55, 492-500. [pdf]
    3. Howell, P.L., Blessing, R.H., Smith, G.D. & Weeks, C.M. (2000). Optimum DREAR and SnB parameters for determining selenium atom substructures, Acta Cryst. D56, 604-617. [pdf]
  • F. Normalization & the DREAR suite
    1. Blessing, R.H., Guo, D.Y. & Langs, D.A. (1998). Intensity statistics and normalization. In Direct methods for solving macromolecular structures, edited by S. Fortier, pp 47-71. Dordrecht: Kluwer Academic Publishers. [pdf]
    2. Blessing, R.H. & Smith, G.D. (1999). Difference structure factor normalization for heavy-atom or anomalous-scattering substructure determinations, J. Appl. Cryst. 32, 664-670. [pdf]
  • G. Substructure and protein phasing
    1. Weeks, C.M., Blessing, R.H., Miller, R., Mungee, R., Potter, S.A., Rappleye, J., Smith, G.D., Xu, H. & Furey, W.  (2002). Towards automated protein structure determination: BnP, the SnB-PHASES interface.  Z. Kristallogr. 217, 686-693.
    2. Weeks, C.M., Adams, P.D., Berendzen, J., Brünger, A.T., Dodson, E.J., Grosse-Kunstleve, R.W., Schneider, T.R., Sheldrick, G.M., Terwilliger, T.C., Turkenburg, M. & Usón, I. (2003). Automatic solution of heavy-atom substructures, Methods Enzymol. 374, 37-83.
    3. Xu, H., Weeks, C.M. & Hauptman, H.A. (2005). Optimizing statistical Shake-and-Bake for Se-atom substructure determination.  Acta Cryst. D61, 90-96. [PubMed]
    4. Xu, H. & Hauptman, H. A. (2006). Recent advances in direct phasing methods for heavy-atom substructure determination.  Acta Cryst. D62, 897-900. [PubMed]
    5. Weeks, C.M. & Furey, W. (2007). Application of direct methods to macromolecular structure solution.  In Macromolecular Crystallography: Conventional and High-Throughput Methods – A Practical Approach, edited by M. Sanderson & J. Skelly.  Oxford: Oxford University Press, pp.129-141. [URL link]
    6. Xu, H. & Weeks, C.M. (2008). Rapid and automated substructure solution by Shake-and-Bake, Acta Cryst. D64, 172-177. [PubMed]