1. HANDS-ON ConSurf! Web-Server: http://consurf.tau.ac.il/http://consurf.tau.ac.il/ The ConSurf webserver

2. Essential input (BLAST, MSA and tree by ConSurf): ConSurf mode: PDB ID\PDB file\model-structure and chain ConSeq mode: a single fasta sequence Essential and optional input: 1.PDB ID\PDB file\model-structure and chain 2.Constructed MSA, with the query sequence included 3.Phylogenetic tree

3. http://consurf.tau.ac.il/ The ConSurf webserver http://consurf.tau.ac.il/results/1322930641/output.php

4. The ConSurf webserver

5. http://consurftest.tau.ac.il/ The ConSurf webserver

8. MSA colored by conservation ConSurf for pymol BLAST & sequences MSA Phylogenetic tree The ConSurf webserver

9. Jmol- Easy web-based viewer

10. * * * View scores

11. View phylogenetic tree Search sequence Change presentation

12. Summary- ConSurf Before using ConSurf, it is recommended to install MDL chime on your computer for the Protein Explorer web-viewer.MDL chime It is highly recommended to install RasTop or PyMol as well.RasTopPyMol

13. MSA Quality ConSurf is dependent on the quality of the MSA. When an MSA is not given by the user, sequences are automatically gathered by PSI-BLAST and aligned by CLUSTALW with default parameters. Even though these alignments are usually good, it is highly recommended to inspect the alignment manually (use BioEdit) and with other tools in order to improve the quality of the evolutionary data.BioEdit Summary- ConSurf

14. A caveat: In some cases the functionally important region may not be conserved at all The peptide-binding groove of the MHC class I heavy chain. PDB id : 2vaa Summary- ConSurf

15. Pre-calculated conservation scores http://consurfdb.tau.ac.il/ Creates MSAs for all proteins in the PDB using a methodology developed from our experience with building MSAs. This process is important to ensure that the conservation scores can be reliably utilized. The database is updated and is extremely user- friendly and easy to use. ConSurf-DB Goldberg et al., 2008

16. ConSurf-DB

17. Goldberg et al., 2008 ConSurf-DB Main Characteristics: 1.Maximum 300 sequences 2.Homologues obtained from SwissProt if there are enough hits, otherwise collected from a clean version of UniProt. 3.MSA performed using MUSCLE 4.Fragments excluded 5.Redundant sequences filtered

18. ConSurf-DB Goldberg et al., 2008 Example: Cytochrome C Panels A&B- ConSurf calculation via the ConSurf- DB (A) and the server with default parameters (B). Panels C&D- conservation calculated via Evolutionary Trace Viewer Wizard and the SiteFiNDER|3D server, respectively.

19. ConSurf-DB PDB id Or protein sequence A list of PDBs

20. ConSurf-DB Select chain

21. ConSurf-DB Results similar to the ConSurf webserver View via FirstGlance in Jmol

22. Producing images

23. High quality via PyMol Open the PDB file downloaded from the PyMol instructions (“File  Open…”) Open the script “consurf_new.py“ downloaded from the PyMol instructions (“File  Run…”) Write “colour_consurf” in the command line Create the image “ray [x] [y]” in the command line Save the image “File  Save image” Producing images

24. Download! Producing images Press

25. Producing images