Tools for integrated sequence-structure analysis with UCSF Chimera

BMC Bioinformatics

Table 1 Chimera results for difficult structure pairs

pair	PDB ID	PDB ID	MM-default	MM-noSS	MM-allSS
1	3chy	2fox	21/1.2, 88/2.2	NR	22/1.1, 88/2.4
2	2aza A	1paz	34/1.2, 79/2.0	8/1.5, 19/2.7	16/1.4, 74/2.3
3	1cew I	1mol A	29/1.0, 73/1.9	6/0.8, 7/1.5	26/0.9, 70/2.0
4	1cid	2rhe	38/1.1, 90/2.0	10/1.3, 21/2.4	11/1.3, 57/2.5
5	1crl	1ede	32/1.3, 184/2.5	6/1.3, 26/3.2	13/1.3, 166/2.6
6	2sim	1nsb A	33/1.2, 257/2.6	4/1.5, 28/3.2	20/1.2, 174/2.9
7	1ten	3hhr B	53/1.1, 82/1.3	4/1.0, 16/2.9	5/0.9, 22/2.9
8	1tie	4fgf	21/1.3, 73/2.2	6/1.1, 22/2.7	15/1.2, 97/2.2
9	2snv	5ptp	32/1.3, 118/2.3	8/1.5, 22/2.4	12/1.4, 103/2.4
10	1gp1 A	2trx A	33/1.0, 89/1.8	5/0.5, 17/2.7	30/1.2, 88/1.7

Results are of the form N/RMSD, where N is the number of residue pairs matched and RMSD is the corresponding alpha-carbon root-mean-square deviation. The first set per column represents the final MatchMaker iteration (after pruning), while the second represents all equivalences from subsequent use of Match -> Align (cutoff 5.0 angstroms). MM-default: MatchMaker with default parameters (BLOSUM-62, 30% secondary structure weighting, prior secondary structure calculation, iteration cutoff 2.0 angstroms; further details are available in the supplementary information [see supplementary.doc]). MM-noSS: same as MM-default except without secondary structure scoring. MM-allSS: same as MM-default except with only the secondary structure term (100% weighting). NR: no results; MatchMaker iteration ended prematurely when the number of residue pairs fell below four.

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