Publications

Magny EG, Pueyo-Marques J, Pearl FMG, Cespedes MA, Niven JE, Bishop SA, Couso, JP.  Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames 2013 Science, 341. pp. 1116-1120.

Richardson CJ, Gao Q, Mitsopoulous C, Zvelebil M, Pearl LH, Pearl
 FMG.  MoKCa database-mutations of kinases in cancer. Nucleic Acids Research 2009; Nucleic Acids Res. 2009 37:D824-31.

Cuff A, Redfern OC, Greene L, Sillitoe I, Lewis T, Dibley M, Reid A, Pearl F, Dalman T, Todd A, Garratt R, Thornton J, Orengo C.  The CATH hierarchy revisited – structural divergence in domain superfamilies and the continuity of fold space. Structure. 2009 Aug 12;17(8):1051-62.

Redfern O, Harrison A, Dallman T, Pearl FMG, Orengo CA.  CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.  PLoS Comput Biol. 2007 3(11):e232.

Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, and Orengo CA. The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. . Nucleic Acids Res. 2007 35:D291-297

Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, Orengo C. The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res. 2005 33:D247-51.

Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C. Recognizing the fold of a protein structure. Bioinformatics. 2003 19:1748-59.

Orengo CA, Pearl FM, Thornton JM. The CATH domain structure database. Methods Biochem Anal. 2003 44:249-71.

Buchan DW, Rison SC, Bray JE, Lee D, Pearl F, Thornton JM, Orengo CA. Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Res. 2003 31:469-73.

Pearl FM, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA.The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res. 2003 31:452-5.

Harrison A, Pearl F, Mott R, Thornton J, Orengo C. Quantifying the similarities within fold space. J Mol Biol. 2002 323:909-26.

Buchan DWA, Shepherd AJ, Lee D, Pearl FMG, Rison SCG, Thornton JM, Orengo CA. Gene3D: Structural assignment for whole genes and genomes using the CATH domain structure database. Genome Research 2002 12:503-514

Pearl FMG, Lee D, Bray JE, Buchan DWA, Shepherd AJ, Orengo CA The CATH extended protein-family database: Providing structural annotations for genome sequences. Protein Science 2002 11:233-244

Orengo CA, Bray JE, Buchan DWA, Harrison A, Lee D, Pearl FMG, Sillitoe I, Todd AE, Thornton JM. The CATH protein family database: A resource for structural and functional annotation of genomes. Proteomics 2002 2:11-21

Orengo CA, Sillitoe I, Reeves G, Pearl FM.Review: What Can Structural Classifications Reveal about Protein Evolution? J Struct Biol, 2001 134:145-65.

Pearl FMG, Martin NM, Bray JE, Buchan DWA, Harrison AP, Lee D, Reeves GA, Shepherd AJ, Sillitoe I, Todd AE, Thornton JM, Orengo CA : A rapid classifcation protocol for the CATH domain database to support structural genomics Nuc Acids Res, 2001 29: 223-227.

Alba MM, Lee D, Pearl FMG, Shepherd AJ, Martin NM, Orengo CA, Kellum P : VIDA: a virus database system for the organization of virus genome open reading frames Nuc Acids Res, 2001 29: 133-136.

Pearl FMG, Todd AE, Bray JE, Martin ACR, Salamov AA, Suwa M, Swindells MB, Thornton JM, Orengo CA (2000): Using the CATH domain database to assign structures and function to the genome sequences. Biochem Soc Trans., 2000 28: 269-275.

Pearl FMG, Lee D, Bray JE, Sillitoe I, Todd AE, Harrison AP, Thornton JM, Orengo CA: Assigning genomic sequences to CATH. Nuc Acids Res, 2000, 28: 277-282.

Bray JE, Todd AE, Pearl FMG, Thornton JM, Orengo CA: The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues. Protein Engineering, 2000, 13: 153-165.

Thornton JM, Orengo CA, Todd AE, Pearl FMG : Protein folds, functions and evolution. J Mol Biol, 1999, 293: 333-342.

Orengo CA, Pearl FMG, Bray JE, Todd AE, Martin AC, LoConte L, Thornton JM : The CATH database provides insights into protein structure/function relationships. Nuc Acids Res, 1999 27: 275-279.

 

BOOK CHAPTERS

Pearl FMG, Thornton JM, Orengo CA (2000): Protein structure classification. Encyclopaedia of life sciences, Macmillan Reference Ltd.

Pearl F & Orengo C (2002): Protein structure classifications. In Bioinformatics: Genes, Proteins & Computers (Orengo CA, Jones DT and Thornton JM (Eds).BIOS.

Orengo, C.A.& Pearl, F. (2003). The CATH Database. in Bourne, P. (ed.) . Structural Bioinformatics. Wiley Publishing.

Pearl F, Bennett C Orengo CA (2004) The CATH database. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (GGPB). Wiley Publishing.

Pearl FMG, Thornton JM, Orengo CA (2007): Protein structure classification. Encyclopaedia of life sciences, Macmillan Reference Ltd.

Orengo, C.A.& Pearl, F. (2009). The CATH Database. in Bourne, P. (ed.) Structural Bioinformatics 2nd Edition. Wiley Publishing.

Publications with abstracts

PubMed