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

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PatchFinder

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

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

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

1 Nimrod et al., Nimrod et al, 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

PatchFinder- Start Page MSA from consurf

PatchFinder- Result Page Detected patch

PatchFinder- Result Page Detected Patches

ConQuass

 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

* 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

ConQuass Upload PDB file Select chain Upload grades file from ConSurf

ConQuass

ConSurf : ConSurf-DB : PatchFinder : Useful Links ConQuass:

BioEdit

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

BioEdit

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