Topology independent protein structural alignment

BMC Bioinformatics

Table 3 Alignment quality

Proteins		HOMSTRAD		FAST			US
PDB(PDB)	PDB(PDB)	N	RMSD	N	M%	RMSD	N	M%	RMSD
1dfaA	1qceA	57	2.5	55	55%	1.2	45	72%	1.1
1hx8A	1hg5A	258	1.1	255	99%	1.1	247	98%	1.0
2ahjA	1rieA	192	4.3	187	89%	2.0	168	99%	1.3
1h7sA	1b63A	105	2.2	98	99%	2.0	96	100%	1.9
1ed9A	1ew2A	403	5.6	343	98%	1.7	252	100%	1.2
1oyc_	2tmdA	330	3.6	284	97%	2.3	193	94%	1.4
1fjnA	1ica_	33	4.7	28	100%	1.9	33	100%	1.8
1tpn_	1fbr_	43	2.4	40	93%	2.2	39	97%	2.2
1e12A	1c3wA	220	1.7	214	97%	1.5	170	100%	0.9
1af6A	1a0tP	377	4.6	323	97%	1.8	281	97%	1.5
1hc1_	1lla_	582	2.3	546	97%	1.7	380	100%	1.4

Table IV from Zhu et al. (2005) with the addition of our alignment results. Zhu et al. chose the following alignment examples to cover a broad range of structural classes. For each alignment, our method returned sequence ordered alignments. N is the number of aligned residues corresponding to each method and M% is the number of aligned residues generated by the corresponding algorithm that are equivalent to HOMSTRAD's aligned residues.

ISSN: 1471-2105