1. EMBL-EBI Eugene Krissinel SSM - MSDfold

2. EMBL-EBI MSDfold (SSM)

3. EMBL-EBI Structure alignment Structure alignment may be defined as identification of residues occupying “equivalent” geometrical positions  Unlike in sequence alignment, residue type is neglected  Used for  measuring the structural similarity  protein classification and functional analysis  database searches

4. EMBL-EBI Method  Many methods are known:  Distance matrix alignment (DALI, Holm & Sander, EBI)  Vector alignment (VAST, Bryant et. al. NCBI)  Depth-first recursive search on SSEs (DEJAVU, Madsen & Kleywegt, Uppsala)  Combinatorial extension (CE, Shindyalov & Bourne, SDSC)  Dynamical programming on C  (Gerstein & Levitt)  Dynamical programming on SSEs (SSA, Singh & Brutlag, Stanford University)  many other  SSM employs a 2-step procedure similar to VAST: A Initial structure alignment and superposition using SSE graph matching B C  - alignment

5. EMBL-EBI E. M. Mitchell et al. (1990) J. Mol. Biol. 212:151     L  SSE graphs differ from conventional chemical graphs only in that they are labelled by vectors of properties. In graph matching, the labels are compared with tolerances chosen empirically. Graph representation of SSEs

6. EMBL-EBI SSE graph matching H1H1 S1S1 S2S2 S3S3 S4S4 H2H2 H1H1 H2H2 H3H3 H4H4 S1S1 H5H5 H6H6 S2S2 S3S3 S4S4 S5S5 S6S6 S7S7 A B H1H1 S1S1 S2S2 H2H2 S3S3 S4S4 S5S5 S6S6 S7S7 H3H3 H4H4 H5H5 H6H6 B H1H1 S1S1 S2S2 S3S3 S4S4 H2H2 A Matching the SSE graphs yields a correspondence between secondary structure elements, that is, groups of residues. The correspondence may be used as initial guess for structure superposition and alignment of individual residues.

7. EMBL-EBI matched helicesmatched strands chain A chain B  SSE-alignment is used as an initial guess for C  -alignment  C  -alignment is an iterative procedure based on the expansion of shortest contacts at best superposition of structures  C  -alignment is a compromise between the alignment length N align and r.m.s.d. Longest contacts are unmapped in order to maximise the Q -score: C  - alignment

8. EMBL-EBI  Based on the same ideas as P -value estimations in VAST  Uses individual Q -scores of SSE deviations  P(S) is the probability of getting a score equal to S or higher at random picking structures from the PDB x1x1 xixi xnxn  P(S) is calibrated on SCOP folds  P(S) is often expressed through Z -score Statistical significance of alignment

9. EMBL-EBI  More than 2 structures are aligned simultaneously  Multiple alignment is not equal to a set of pairwise alignments  Helps to identify common structure motifs for a whole family of structures Multiple structure alignment

10. EMBL-EBI  Based on the analysis of SSE correspondences in the course of all-to-all pairwise alignments  SSEs with number of successful pairwise alignments less then maximal are gradually removed in repeating iterations  Multiple SSE alignment is followed by multiple C  -alignment in 3D Algorithm of multiple alignment Number of successful pairwise alignments 3 3 3 2 1 Do not align ABC

11. EMBL-EBI  Table of matched Secondary Structure Elements  Table of matched backbone C  -atoms with distances between them at best structure superposition  Rotation-translation matrix of best structure superposition  r.m.s.d. of C  -alignment  Length of C  -alignment N align  Number of gaps in C  -alignment  Quality score Q  Statistical significance scores P(S), Z  Sequence identity SSM output

12. EMBL-EBI http://www.ebi.ac.uk/msd-srv/ssm SSM server map

13. EMBL-EBI http://www.ebi.ac.uk/msd-srv/ssm 6. Submit 1. Set Query: PDB/SCOP entry Coordinate file List of pairs 2. Set Target: PDB/SCOP entry Coordinate file PDB/SCOP archive SCOP subset User’s archive 3. Select chain(s) or a domain 5. Set match options 4. Set similarity level SSM submission form

14. EMBL-EBI SSM wait page

15. EMBL-EBI Match details List of matches

16. EMBL-EBI View in Rasmol Download superposed Match details

17. EMBL-EBI Links to Web services related to the structure SSE alignment

18. EMBL-EBI C  alignment

19. EMBL-EBI  r.m.s.d. - good measure only if all residues are aligned  N align - not indicative, subject to alignment procedure and parameters  Q -score - an attempt to balance N align and r.m.s.d. :  P(S), Z - indicates only the statistical significance of matches and depends on the calibration database  ???????????????? Measuring the structure similarity

20. EMBL-EBI Q-score vs. r.m.s.d. and N align (1SAR:A)

21. EMBL-EBI Maximal Q-score d1di2a_ (69 res) Q-score0.213 RMSD2.43 N align 67/184 Lowest RMSD d1emn_1 (43 res) Q-score0.019 RMSD0.9 N align 13/184 Highest N align d1e1xb_ (449 res) Q-score0.02 RMSD5.82 N align 89/184 Scoring at low structural similarity - 1KNO:A vs SCOP 1.61

22. EMBL-EBI Performance data

23. EMBL-EBI Acknowledgement This work has been supported by Collaborative Computational Project Number 4 (CCP4) of the UK Biotechnology and Biological Sciences Research Council.

24. EMBL-EBI Number of SSM users