1. PatchFinder

2. The ConSurf web-server calculates the evolutionary rate for each position in the protein. Surface clusters of spatially close & conserved residues are often found. PatchFinder

3. Patch- a spatially continuous cluster of surface residues. Problems: – Subjectivity of boundaries. – Difficult to apply on large datasets PatchFinder

4. Nimrod et al., 2005 Nimrod et al., 2008 PatchFinder An algorithm for the identification of conserved patches in proteins of known 3D structure.

5. 1 Nimrod et al., 2005 2 Nimrod et al, 2008 3 Mayrose et al., 2004 (1) Assignment of conservation scores (Rate4Site3) (4) Identification of non- overlapping secondary patches (2) Identification of exposed residues (3) Extraction of the surface patch of conserved residues with the highest statistical significance (ML-patch). Input: 1. Protein Structure2. Multiple sequence alignment (MSA) PatchFinder 1,2

6. PatchFinder- Start Page MSA from consurf

7. PatchFinder- Result Page Detected patch

8. PatchFinder- Result Page Detected Patches

9. ConQuass

10.  It is well-known that evolutionary conserved residues tend to be buried in the structure core, and variable residues tend to be exposed. PDB: 1ute (phosphatase) ConQuass

11. * From The PISCES webserver - resolution cutoff 3.0Å, R-factor cutoff 0.3.  This can be shown quantitatively when collecting statistics for all high-quality PDB structures * (by naccess) ConQuass

12. 0.13 -0.11

13. ConQuass http://bental.tau.ac.il/ConQuass/conquass.php Upload PDB file Select chain Upload grades file from ConSurf

14. ConQuass http://bental.tau.ac.il/ConQuass/conquass.php 0.166 0.146

15. ConSurf : http://consurf.tau.ac.il/ ConSurf-DB : http://consurfdb.tau.ac.il/ PatchFinder : http://patchfinder.tau.ac.il/ Useful Links ConQuass: http://patchfinder.tau.ac.il/

16. BioEdit

17. MSAs cannot be easily examined without an appropriate program The programs enable easy viewing, coloring, presenting and editing of MSAs consisting of a large number of sequences. Some viewers are also able of running other programs, e.g. performing an alignment when sequences are given as input. Two of the top viewers are: BioEdit- briefly presented next JalView

18. BioEdit http://www.mbio.ncsu.edu/BioEdit/bioedit.html

19. Find a specific sequence: “Edit-> search -> in titles” Erase\add sequences: “Edit-> cut\paste\delete sequence” “Sequence Identity matrix” under “Alignment”- useful for a rough evaluation of distances within the alignment. After taking out sequences, “Minimize Alignment” under “Alignment” takes out unessential gaps. Can save an image using: “File -> Graphic View” & then “Edit -> Copy page as BITMAP” BioEdit