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.

Meng et al. BMC Bioinformatics 2006 7:339   doi:10.1186/1471-2105-7-339

Open Data