User talk:Darek Kedra/sandbox 6

• SARF [65],
• Combinatorial Extension (CE) [66],
• DALI [67],
• Structural [68],
• VAST [69],
• FAST [70]
• MAMMOTH [71]

have the great advantage of using atomic coordinates for both query and target proteins.

From: B RIEFINGS IN BIOINF ORMATICS . VOL 8. NO 2. 78 ^ 87 doi:10.1093/bib/bbl032 Advance Access publication September 26, 2006 The WWWH of remote homolog detection: The state of the art Piero Fariselli, Ivan Rossi, Emidio Capriotti and Rita Casadio

64. Bujnicki JM, Elofsson A, Fischer D, et al. Structure prediction meta server. Bioinformatics 2001;17:750 65. Alexandrov NN. SARFing the PDB. Protein Eng 1996;9:727 66. Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal

   path. Protein Eng 1998;11:739

67. Holm L, Sander C. Protein folds and families: sequence and structure alignments. Nucleic Acids Res 1999;27:244 68. Levitt M, Gerstein M. A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci USA 1998;95:5913

69. Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol 1996;6:377. 70. Zhu J, Weng Z. FAST: a novel protein structure alignment algorithm. Proteins 2005;58:618 71. Lupyan D, Leo-Macias A, Ortiz AR. A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics 2005;21:3255

72. Siew N, Elofsson A, Rychlewski L, et al. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 2000;16:776