Pound-Wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?

Structure

Volumn 11, Issue 9, 2003, Pages 1051-1059

  Kleywegt, Gerard J ^a   Henrick, Kim ^b   Dodson, Eleanor J ^c   Van Aalten, Daan M F ^d  

^a UPPSALA UNIVERSITY   (Sweden)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF YORK   (United Kingdom)

^d UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; PROTEIN;

AB INITIO CALCULATION; ACCURACY; ANALYTICAL ERROR; BIOINFORMATICS; COMPUTER PROGRAM; COMPUTER SIMULATION; EMPIRICISM; GEOMETRY; INTERMETHOD COMPARISON; MACROMOLECULE; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; PARAMETER; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN STRUCTURE; REVIEW; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 0041333142     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(03)00186-2     Document Type: Note

References (54)

1. van Aalten D.M.F., Bywater R., Findlay J.B.C., Hendlich M., Hooft R.W.W., Vriend G. PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput. Aided Mol. Des. 10:1996;255-262.
2. Allen F.H., Bellard S., Brice M.D., Cartwright B.A., Doubleday A., Higgs H., Hummelink T., Hummelink-Peters B.G., Kennard O., Motherwell W.D.S.et al. The Cambridge Crystallographic Data Centre. computer-based search, retrieval, analysis and display of information Acta Crystallogr. B35:1979;2331-2339.
3. Allen F.H., Kennard O., Watson D.G., Brammer L., Orpen A.G., Taylor R. Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds. J. Chem. Soc. Perkin Trans. II. 1987:1987;S1-S19.
4. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242.
5. Berman H.M., Westbrook J., Feng Z., Iype L., Schneider B., Zardecki C. The Nucleic Acid Database. Acta Crystallogr. D58:2002;889-898.
6. Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F. Jr., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank. a computer-based archival file for macromolecular structures J. Mol. Biol. 112:1977;535-542.
7. Bertini I., Cavallaro G., Luchinat C., Poli I. A use of Ramachandran potentials in protein solution structure determinations. J. Biomol. NMR. 26:2003;355-366.
8. Bohne A., Lang E., von der Lieth C.W. SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides. Bioinformatics. 15:1999;767-768.
9. Boström J. Reproducing the conformations of protein-bound ligands. a critical evaluation of several popular conformational searching tools J. Comput. Aided Mol. Des. 15:2001;1137-1152.
10. Boutselakis H., Dimitropoulos D., Fillon J., Golovin A., Henrick K., Hussain A., Ionides J., John M., Keller P.A., Krissinel E.et al. E-msd. the european bioinformatics institute macromolecular structure database Nucleic Acids Res. 31:2003;458-462.
11. Brünger A.T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 235:1987;458-460.
12. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S.et al. Crystallography and NMR System. a new software suite for macromolecular structure determination Acta Crystallogr. D54:1998;905-921.
13. Bruno I.J., Cole J.C., Edgington P.R., Kessler M., Macrae C.F., McCabe P., Pearson J., Taylor R. New software for searching the Cambridge Structural Database and visualizing crystal structures. Acta Crystallogr. B58:2002;389-397.
14. Clowney L., Westbrook J.D., Berman H.M. CIF applications. XI. A La Mode. a ligand and monomer object data environment. I. Automated construction of mmCIF monomer and ligand models J. Appl. Crystallogr. 32:1999;125-133.
15. The CCP4 suite. programs for protein crystallography Acta Crystallogr. D50:1994;760-763.
16. Davis A.M., Teague S.J., Kleywegt G.J. Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew. Chem. Int. Ed. Engl. 42:2003;2718-2736.
17. Engh R.A., Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A47:1991;392-400.
18. Engh R.A., Huber R. Structure quality and target parameters. Rossman M.G., Arnold E. International Tables for Crystallography. Volume F. Crystallography of Biological Macromolecules:2001;382-392 Kluwer, Dordrecht, The Netherlands.
19. Gasteiger J., Rudolph C., Sadowski J. Automatic generation of 3D-atomic coordinates for organic molecules. Tetrahedron Comp. Method. 3:1990;537-547.
20. Greaves R.B., Vagin A.A., Dodson E.J. Automated production of small-molecule dictionaries for use in crystallographic refinements. Acta Crystallogr. D55:1999;1335-1339.
21. van Gunsteren W.F., Berendsen H.J.C. GROMOS Manual. BIOMOS, Biomolecular Software, Laboratory of Physical Chemistry. 1987;University of Groningen Press, Groningen, The Netherlands.
22. Harding M.M. Geometry of metal-ligand interactions in proteins. Acta Crystallogr. D57:2001;401-411.
23. Hendrickson W.A., Konnert J.H. Incorporation of stereochemical information into crystallographic refinement. Diamond R., Ramaseshan S., Venkatesan K. Computing in Crystallography. 1980;13 Indian Academy of Science, Bangalore, India. 01-13.25.
24. Hendrickson W.A. Stereochemically restrained refinement of macromolecular structures. Methods Enzymol. 115:1985;252-270.
25. Hooft R.W.W., Vriend G., Sander C., Abola E.E. Errors in protein structures. Nature. 381:1996;272.
26. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47:1991;110-119.
27. Kleywegt G.J. Validation of protein crystal structures. Acta Crystallogr. D56:2000;249-265.
28. Kleywegt G.J., Jones T.A. Databases in protein crystallography. Acta Crystallogr. D54:1998;1119-1131.
29. Kuszewski J., Gronenborn A.M., Clore G.M. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases. Protein Sci. 5:1996;1067-1080.
30. Kuszewski J., Gronenborn A.M., Clore G.M. Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids. J. Magn. Reson. 125:1997;171-177.
31. Lancaster C.R.D., Michel H. The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB. Structure. 5:1997;1339-1359.
32. Laskowski R.A., Moss D.S., Thornton J.M. Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol. 231:1993;1049-1067.
33. Lide D.R. CRC Handbook of Chemistry and Physics. 75th Edition:1995;CRC Press, Boca Raton, FL.
34. Lindahl E., Hess B., van der Spoel D. Gromacs 3.0. a package for molecular simulation and trajectory analysis J. Mol. Model. 7:2001;306-317.
35. McRee D.E. XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125:1999;156-165.
36. Mitchell J.B., Smith J. D-amino acid residues in peptides and proteins. Proteins Struct. Funct. Genet. 50:2003;563-571.
37. Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53:1997;240-255.
38. Nilsson K., Lecerof D., Sigfridsson E., Ryde U. An automatic method to generate force-field parameters for hetero-compounds. Acta Crystallogr. D59:2003;274-289.
39. Nissink J.W., Murray C., Hartshorn M., Verdonk M.L., Cole J.C., Taylor R. A new test set for validating predictions of protein-ligand interaction. Proteins Struct. Funct. Genet. 49:2002;457-471.
40. Oldfield T.J. A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent. Acta Crystallogr. D57:2001;82-94.
41. Parkinson G., Vojtechovsky J., Clowney L., Brünger A.T., Berman H.M. New parameters for the refinement of nucleic acid-containing structures. Acta Crystallogr. D52:1996;57-64.
42. Priestle J.P. Stereochemical dictionaries for protein structure refinement and model building. Structure. 2:1994;911-913.
43. Priestle J.P. Improved dihedral-angle restraints for protein structure refinement. J. Appl. Crystallogr. 36:2003;34-42.
44. Ricketts E.M., Bradshaw J., Hann M., Hayes F., Tanna N., Ricketts D.M. Comparison of conformations of small molecule structures from the Protein Data Bank with those generated by Concord, Cobra, ChemDBS-3D, and Converter and those extracted from the Cambridge Structural Database. J. Chem. Inf. Comput. Sci. 33:1993;905-925.
45. Sadowski J., Gasteiger J., Klebe G. Comparison of automatic three-dimensional model builders using 639 X-ray structures. J. Chem. Inf. Comput. Sci. 34:1994;1000-1008.
46. Schultze P., Feigon J. Chirality errors in nucleic acid structures. Nature. 387:1997;668.
47. Sheldrick G.M., Schneider T.R. Shelxl. high-resolution refinement Methods Enzymol. 277:1997;319-344.
48. Tronrud D.E. The TNT refinement package. Methods Enzymol. 277:1997;306-319.
49. Vagin A.A., Murshudov G.N., Strokopytov B.V. Blanc. the program suite for protein crystallography J. Appl. Crystallogr. 31:1998;98-102.
50. Wallace A.C., Laskowski R.A., Thornton J.M. Ligplot. a program to generate schematic diagrams of protein-ligand interactions Protein Eng. 8:1995;127-134.
51. Waser J. Least-squares refinement with subsidiary conditions. Acta Crystallogr. 16:1963;1091-1094.
52. Watenpaugh K.D., Sieker L.C., Herriott J.R., Jensen L.H. Refinement of the model of a protein. rubredoxin at 1.5 Å resolution Acta Crystallogr. B29:1973;943-956.
53. Weininger D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28:1988;31-36.
54. Weininger D., Weininger A., Weininger J.L. SMILES. 2. Algorithm for generation of unique SMILES notation. J. Chem. Inf. Comput. Sci. 29:1989;97-101.