Protein structure determination using a database of interatomic distance probabilities

Protein Science

Volumn 8, Issue 12, 1999, Pages 2720-2727

  Wall, Michael E ^a,c   Subramaniam, Shankar ^b,d   Phillips Jr , George N ^a  

^a RICE UNIVERSITY   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Knowledge based modeling; Low resolution; Molecular dynamics; Structure refinement; X ray crystallography

Indexed keywords

ARTICLE; CRYSTAL STRUCTURE; DATA BASE; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 0033458068     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.12.2720     Document Type: Article

References (28)

1. Bernstein FC, Koetzle TF, Williams GJB, Myer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structure. J Mol Biol 112:535-542.
2. Blundell TL, Sibanda BL, Sternberg MJE, Thornton JM. 1987. Knowledge-based prediction of protein structures and design of novel molecules. Nature 323:347-352.
3. Browne WJ, North ACT, Philips DC, Brew K, Vanaman TC, Hill RL. 1969. A possible three-dimensional structure of bovine β-lactalbumin based on that of hen's egg white lysozyme. J Mol Biol 42:65-86.
4. Brünger AT. 1992. Free R-value - A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472-475.
5. Brünger AT. 1993. X-PLOR version 3.1: A system for X-ray crystallography and NMR. New Haven, Connecticut: Yale University Press.
6. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kuntsleve RW, Jiang JS, Kusrewski J, Nilges M, Pannu NS, et al. 1998. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D54:905-921.
7. Brünger AT, Kuriyan J, Karplus M. 1987. Crystallographic R factor refinement by molecular dynamics. Science 235:458-460.
8. Engh RA, Huber R. 1991. Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Crystallogr A47:392-400.
9. Hendrickson WA, Konnert JH. 1980. Incorporation of stereochemical information into crystallographic refinement. In: Diamond R, Ramaseshan S, Venkatesan K, eds. Computing in crystallography. Bangalore, India: Indian Academy of Sciences. pp 13.01-13.23.
10. Jones DT, Thornton JM. 1996. Potential energy functions for threading. Curr Opin Struct Riol 6:210-216.
11. Minor DL Jr. Kim PS. 1996. Context-dependent secondary structure formation of a designed protein sequence. Nature 380:730-734.
12. Rice LM, Brünger AT. 1994. Torsion angle dynamics - Reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 19:277-290.
13. Rojnuckarin A, Subramanian S. 1999. Knowledge-based interaction potentials for proteins. Proteins 36:54-67.
14. Romo TD. 1998. Identification and modeling of protein conformational substates [PhD thesis]. Rice University, Houston, Texas.
15. Sack JS. 1988. CHAIN - A crystallographic modeling program. J Mol Graph 6:244-245.
16. Sanchez R, Sali A, 1997. Advances in comparative protein-structure modelling. Curr Opin Struct Biol 7:206-214.
17. Schutt CE. 1987. Muscle regulation - Movement on the Aufbaubahn. Nature 325:757-758.
18. Sheldrick GM, Schneider TR. 1997. SHELXL: High-resolution refinement. Methods Enzymol 277B:319-343.
19. Silverman BW. 1982. Algorithm AS 176. Kernel density estimation using the fast Fourier transform. Appl Stat 31:93-99.
20. Sippl MJ. 1990. Calculation of conformational ensembles from potentials of mean force - An approach to the knowledge-based prediction of local structures in globular-proteins. J Mol Biol 213:859-883.
21. Sippl M. 1993. Recognition of errors in 3-dimensional structures of proteins. Proteins 17:355-362.
22. Soman J, Tao T, Phillips GN Jr. 1999. Conformational variation of calcium-bound troponin C. Proteins. In press.
23. Subramaniam S, Tcheng DK, Fenton JM. 1996. In: States DJ, Agarwal P, Gassterland T, Hunter L, Smith RF. eds. Proceedings of the fourth international conference on intelligent systems in molecular biology. St. Louis, Menlo Park, CA: AAAI Press. pp 218-229. (Currently available at http://glycine. ncsa.uiuc.edu/doc/ISMB96-PDF.html.)
24. Terwilliger TC, Waldo G, Peat TS, Newman JM, Chu K, Berendzen J. 1998. Class-directed structure determination: Foundation for a protein structure initiative. Protein Sci 7:1851-1856.
25. Tronrud DE. 1997. The TNT refinement package. Methods Enzymol 277B:306-319.
26. Volkenstein MV. 1963. Statistics of polymeric chains. New York: Interscience. (Translated from Russian by Timasheff SN, Timasheff MJ.)
27. Wall ME, Garage JB, Phillips GN Jr. 1997. Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. Structure 5:1599-1612.
28. Word JM, Lovell SC, Richardson JS, Richardson DC. 1999. Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285:1735-1747.