Biology Reference
In-Depth Information
50. Cannone JJ, Subramanian S, Schnare MN,
Collett JR, D'Souza LM, Du Y, Feng B, Lin
N, Madabusi LV, Muller KM, Pande N, Shang
Z, Yu N, Gutell RR (2002) The comparative
RNA web (CRW) site: an online database of
comparative sequence and structure informa-
tion for ribosomal, intron, and other RNAs.
BMC Bioinformatics 3:2
51. O'Sullivan O, Suhre K, Abergel C, Higgins
DG, Notredame C (2004) 3DCoffee: combin-
ing protein sequences and structures within
multiple sequence alignments. J Mol Biol
340:385-395
52. Pei J, Kim BH, Grishin NV (2008) PRO-
MALS3D: a tool for multiple protein sequence
and structure alignments. Nucleic Acids Res
36:2295-2300
53. Standley DM, Toh H, Nakamura H (2004)
Detecting local structural similarity in proteins
by maximizing number of equivalent residues.
Proteins 57:381-391
54. Taylor WR, Orengo CA (1989) Protein struc-
ture alignment. J Mol Biol 208:1-22
55. Orengo CA, Taylor WR (1993) A local align-
ment method for protein structure motifs.
J Mol Biol 233:488-497
56. Toh H (1997) Introduction of a distance cut-
off into structural alignment by the double
dynamic programming algorithm. Comput
Appl Biosci 13:387-396
57. Katoh K, Asimenos G, Toh H (2009) Multiple
alignment of DNA sequences with MAFFT.
Methods Mol Biol 537:39-64
