Information Technology Reference
In-Depth Information
[33]
King, S.M. & Johnson, W.C. Jr., (1999) Assigning Secondary Structure From Protein Coordinate Data.
Proteins Struct. Func. Gen.
35, 313-320
[34]
Sun, Z. & Jiang, B., (1996) Patterns and Conformations of Commonly Occurring Supersecondary
Structures (Basic Motifs) in the Protein Data Bank.
J. Prot. Chem.
15, 675-690
[35]
Sibanda, B.L. & Thornton, J.M., (1985) β-Hairpin Families in Globular Proteins.
Nature
316, 170-174
[36]
Boutonnet, N.S., Kajava, A.V. & Rooman, M.J., (1998) Structural Classification of
ααβ
and
ββα
Supersecondary Structure Units in Proteins.
Prot. Struct. Func. Gen.
30, 193-212
[37]
Zhang, C. & Kim, S-H., (2000) A Comprehensive Analysis of the Greek-Key Motifs in Protein Barrels
and Sandwiches.
Prot. Struct. Func. Gen
. 40, 409-414
[38]
Epimov, A., (1995) Structural Similarity Between 2-Layer Alpha/Beta-Proteins and Beta-Proteins.
J.
Mol. Biol.
245,402-415
Branden, C. & Tooze, J., (1999)
Introduction to Protein Structure
. 2
nd
Ed. Garland Publishing, New
York.
[39]
[40]
Kretsinger, R.H., (1980) Structure and Evolution of Calcium-Modulated-Proteins.
Crit. Rev. Biochem
.
8, 119-174
[41]
Hatanaka, H., Oka, M., Kohda, D., Tate, S., Suda, A., Tamiys, N. & Inagaki, F., (1994) Tertiary
Structure of Erabutoxin b in Aqueous Solution Elucidated by Nuclear Magnetic Resonance.
J. Mol.
Biol.
240, 155-166
[42]
Cates, M.S., Berry, M.B., Ho, E., Li, J.D., Potter, J.D. & Phillips, G.N. Jr., (1999) Metal Ion Affinity
and Specificity in EF- Hand Proteins: Coordination Geometry and Domain Placticity in Parvalbumin.
Structure.
7, 1269-1278
[43]
Harrison, A., Pearl, F., Mott, R., Thornton, J. & Orengo, C.A., (2002) Quantifying the Similarities
Within Fold Space.
J. Mol. Biol.
323, 909-926
[44]
Flores, T.P., Orengo, C.A. & Thornton, J.M., (1993) Conformational Characteristics of Structurally
Similar Proteins.
Protein Sci.
7, 31-37
[45]
Orengo, C.A., (1994) Classification of Protein Folds.
Curr. Op. Struct. Biol.
4,429-440
[46]
Taylor, W.W., & Orengo, C.A., (1989) Protein Structure Alignment.
J. Mol. Biol.
208,1-22
[47]
Madej, T., Gibrat, J-F. & Bryant, S.H., (1995) Threading a Database of Protein Cores.
Proteins Struct.
Func. Genet
. 23, 356-359
[48]
Holm, L. & Sander, C., (1993) Protein Structure Comparison by Alignment of Distance Matrices.
J.
Mol. Biol.
223,123-138
[49]
Holm, L. & Sander, C., (1996) Mapping the Protein Universe.
Science
273, 595-602
[50]
Holm, L. & Sander, C., (1997) Dali/FSSP Classification of Three-Dimensional Protein Folds.
Nucleic
Acids Res.
25, 231-234
[51]
Murzin, A. G., Lesk, A. M. & Chothia, C., (1992).
-Trefoil Fold. Patterns of Structure and Sequence
in the Kunitz Inhibitors, Interleukins-1b and 1a and Fibroblast Growth Factors.
J. Mol. Biol
. 223, 531-
543
β
[52]
Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. & Thornton, J.M., (1997) CATH-
A Hierarchic Classification of Protein Domain Structures.
Structure
. 5, 1093-1108
[53]
Dietmann, S., Park, J., Notredame, C., Hegar, A., Lappe, M. & Holm, L., (2001) A Fully Automatic
Evolutionary Classification of Protein Folds: Dali Domain Dictionary Version 3.
Nucleic Acids Res.
29, 55-57
[54]
Day, R., Beck, D.A.C., Roger, S. & Daggett, V., (2003) A Consensus View of Fold Space: Combining
SCOP, CATH and the Dali Domain Dictionary.
Protein Sci.
12, 2150-2160
[55]
Hadley, C. & Jones, D.T., (1999) A Systematic Comparison of Protein Structure Classifications:
SCOP, CATH and FSSP.
Structure
7, 1099-1112
[56]
Domany, E., (2002) Automated Assignment of SCOP and
CATH protein structure classifications from FSSP scores.
Proteins: Stuct. Func. Gen.
46, 405-415
[57] Orengo, C.A., Jones, D. & Thornton, J.M., (1994) Protein Superfamilies and Domain Super-folds.
Nature
372,631-634
[58] Hamada K., Bethge P.H., Mathews F.S., (1995) Refined Structure of Cytochrome b562 from
Escherichia coli
at 1.4-A Resolution.
J. Mol. Biol.
247, 947-962
Getz, G., Vendruscolo, M., Sachs, D.
&
[59]
Bhyravbhatla, B., Watowich, S.J. & Caspar D.L., (1998) Refined Atomic Model of the Four-Layer
Aggregate of the Tobacco Mosaic Virus Coat Protein at 2.4 Å Resolution.
Biophys. J
. 74, 604- 615
[60]
Safo M.K. & Abraham D.J., (2001) The X-ray Structure Determination of Bovine Carbonmonoxy
Hemoglobin at 2.1 Å Resolution and its Relationship to the Quaternary Structures of Other
Hemoglobin Crystal Forms.
Protein Sci
. 10, 1091-1099
[61]
Duerring, M., Schmidt, G.B. & Huber R., (1991) Isolation, Crystallization, Crystal Structure Analysis
and Refinement of Constitutive C-Phycocyanin from the Chromatically Adapting Cyanobacterium
Fremyella diplosiphon
at 1.66-A Resolution.
J. Mol. Biol
. 217, 577-592