REFERENCES

Current reference

When using the current version of JOY, please cite:

Mizuguchi, K., Deane, C.M., Johnson, M.S., Blundell, T.L. & Overington, J.P., (1998). JOY: protein sequence-structure representation and analysis. Bioinformatics, 14, 617-623.

 

Early work on JOY and the alignment database

J.P. Overington, M.S. Johnson, A. Sali, and T.L. Blundell, (1990), ``Tertiary structural constraints on protein evolutionary diversity; Templates, key residues and structure prediction,'' Proc. Roy. Soc. Lond., B 241, pp. 132-145.

J.P. Overington, M. Johnson, C. Topham, A. McLeod, A. Sali, Z.-Y. Zhu, L. Sibanda, T. Blundell, (1990), ``Applications of environment specific amino acid substitution tables to identification of key residues in protein tertiary structure,'' Curr. Sci., 59, pp. 867-874.

A. Sali, J.P. Overington, M.S. Johnson, and T.L. Blundell, (1990), ``From comparisons of protein sequences and structures to protein modelling and design,'' Trends Biochem. Sci., 15, pp. 235-240. (Also published in: Proteins: Form and Function, (1990), ed. R. Bradshaw and M. Purton, Elsevier Trends Journals, Cambridge, pp. 163-171).

A.-M. Hoffren, M. Saloheimo, P. Thomas, J.P. Overington, M.S. Johnson, J.K.C. Knowles, and T.L. Blundell, (1991), ``Modelling the lignin peroxidase LIII of Phlebia radiata using a knowledge-based approach,'' J. Chim. Phys., 88, pp. 2659-2662.

J.P. Overington, D. Donnelly, M.S. Johnson, A. Sali, and T.L. Blundell,(1991), ``Environment specific amino acid substitution tables: Tertiary templates and prediction of protein folds,'' Protein Science, 1, pp. 216-226.

M.S. Johnson, J.P. Overington, and T.L. Blundell, (1993), ``Alignment and searching for common protein folds using a data bank of structural templates,'' J. Mol. Biol., 231, pp. 735-752

J.P. Overington, Z.-Y. Zhu, A. Sali, M.S. Johnson, R. Sowdhamini, G.V. Louie, and T.L. Blundell, (1993), ``Molecular recognition in protein families: A database of aligned three-dimensional structures of related proteins,'' Biochem. Soc. Trans., 21, pp. 597-604.

C.M. Topham, A. McLeod, F. Eisenmenger, J.P. Overington, M.S. Johnson, and T.L. Blundell, (1993), ``Fragment ranking in modelling of protein structure: Conformationally constrained environmental amino acid substitution tables,'' J. Mol. Biol., 229, pp. 194-220.

A. Sali, and T.L. Blundell, (1993), ``Comparative protein modelling by satisfaction of spatial restraints,'' J. Mol. Biol., 234, pp. 779-815.

A. Sali, and J.P. Overington (1994), ``Derivation of rules for comparative protein modelling from a database of protein structure alignments'' Prot. Sci., 3, pp. 1582-1596.

 

Recent applications and related work

Miguel, R.N., Shi, J., Mizuguchi, K. (2002). Protein fold recognition and comparative modelling using HOMSTRAD, JOY and FUUGE. In Protein Structure Prediction: Bioinformatic Approach. International University Line publishers, La Jolla. (in press)

Williams, M.G., Shirai, H., Shi, J., Nagendra, H.G., Mueller, J., Mizuguchi, K., Miguel, R.N., Lovell, S.C., Innis, C.A., Deane, C.M., Chen, L., Campillo, N., Burke, D.F., Blundell, T.L., de Bakker, P.I.W. (2001) Sequence-structure homology recognition by iterative alignment refinement and comparative modelling. Proteins (in press).

de Bakker, P.I.W., Bateman, A., Burke, D.F., Miguel, R.N., Mizuguchi, K., Shik J. Shirai, H., Blundell, T.L. (2001) HOMSTRAD: Adding sequence information to structure-based alignments of homologous proteins families. Bioinformatics 17, 748-749..

Parker, J.S., Mizuguchi, K., & Gay, N.J. (2001) A family of proteins related to Spätzle, the Toll receptor ligand, are encoded in the Drosophila genome. Proteins 45, 71-80.

Shirai, H., Blundell, T.L. & Mizuguchi, K. (2001) A novel superfamily of enzymes that catalyze the modification of guanidino groups. Trends Biochem. Sci. 26, 465-468.

Shi, J., Blundell, T.L. & Mizuguchi, K. (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310, 243-257.

Mizuguchi, K., Dhanaraj, V., Blundell, T.L, & Murzin, A.G., (1999). N-ethylmaleimide-sensitive fusion protein (NSF) and CDC48 confirmed as members of the double-psi b -barrel aspartate decarboxylase/formate dehydrogenase family. Structure 7, R215-R216.

Marino-Buslje, C., Martin-Martinez, M., Mizuguchi, K., Siddle, K. & Blundell, T.L., (1999). The insulin receptor: from sequence to structure and function. Biochemical Society Transaction 27, 715-726.

Burke, D.F., Deane, C.M., Nagarajaram, H.A., Campillo, N., Martin-Martinez, M., Mendes, J., Molina, F., Perry, J., Reddy, B.V.B., Soares, C.M., Steward, R.E., Williams, M., Carrondo, M.A., Blundell, T.L., Mizuguchi, K., (1999). An iterative structure-assisted approach to sequence alignment and comparative modelling. Proteins Suppl 3, 55-60.

Castillo, R.M., Mizuguchi, K., Dhanaraj, V., Albert, A., Blundell, T.L. & Murzin, A.G., (1999). A six-stranded double-psi b barrel is shared by several protein superfamilies. Structure, 7, 227-236.

Marino-Buslje, C., Mizuguchi, K., Siddle, K. & Blundell, T.L., (1998). A third fibronectine type III domain in the extracellular region of the insulin receptor family. FEBS letters, 441, 331-336.

Sowdhamini, R., Burke, D.F., Huang, J.-F., Mizuguchi, K., Nagarajaram, H.A., Srinivasan, N., Steward, R.E. & Blundell, T.L., (1998). CAMPASS: A database of structurally aligned protein superfamilies. Structure, 6, 1087-1094.

Sowdhamini, R., Burke, D.F., Deane, C.M. Huang, J.-F., Mizuguchi, K., Nagarajaram, H.A, Overington, J.P., Srinivasan, N., Steward, R.E. & Blundell, T.L., (1998). Protein 3D structural databases: domains, structurally aligned homologues and superfamilies. Acta Cryst. D54, 1168-1177.

Mizuguchi, K., Parker, J.S., Blundell, T.L. & Gay, N.J., (1998). Getting knotted: a model for the structure and activation of Spätzle. Trends Biochem. Sci., 23, 239-242.

Mizuguchi, K., Deane, C.M., Blundell, T.L. & Overington, J.P., (1998). HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci., 7, 2469-2471.


Revised: 15 Feb 2002 .

joy@mizuguchilab.org