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Welcome from ec2-54-227-5-234.compute-1.amazonaws.com.
This is version 1.20 of the Surface Entropy Reduction prediction (SERp) server from January 2007. This exploratory tool aims to aid identification of sites that are most suitable for mutation designed to enhance crystallizability by a Surface Entropy Reduction approach. More Info: introduction page, publication reference.

Please send bug reports, questions and feedback to adminstrator <ser@mbi.ucla.edu>. To submit multiple sequences in FASTA format, use the Batch Submission page.

The following graphs are provided to aid visualization of the proposed mutation sites, and to help understand the contribution of each factor. Taken together, all factors determine which sites are most suitable for mutation. [More...]

Overall Score -- Stacked Graph Showing Contribution of each Primary Analysis: [?]

Ideal mutation candidates are non-conserved, high entropy residues that lie in surface-exposed, entropy-rich regions of the protein. Residues proposed for mutation within a high entropy cluster are shaded green. Target low-entropy patch is shaded gray.

Top: Score contribution of the following three factors to the overall score at each residue position:
  • Secondary Structure. Contribution from the PSIPRED prediction of coil regions.
  • Entropy Average. Contribution from the sidechain entropy average computation in a window of 3 residues. [Details]
  • Conserved and mutated residues. Contributions from the BLAST search. [Details]

Bottom:
Top row, before mutation. Bottom row, after proposed mutation.
  • High entropy residues (KEQD) are shown in pink.
  • Mutable residues (KEQ(0.33)) in red.
  • Residues proposed for mutation are in green.
  • Low entropy target residues (A) are shown in orange.




Entropy Average: [?] [Back to Top]

Normalized sidechain entropy average at each residue position as given by Sternberg, computed in a 3 residue window. Residues with entropy average above the user-specified cutoff contribute to the overall score.



Secondary Structure -- Helix, Strand and Coil Regions: [?] [Back to Top]

Secondary structure predicion as returned by PSIPRED. Stacked graph of condidences for Helix, Strand or Coil at each position in the sequence. Only residues with coil confidence above the user-specified cutoff contribute to the overall score.



Blast Results -- Conserved and Mutated Residues: [?] [Back to Top]

Number of sequences found by the PSI-BLAST search containing a conserved residue (same as submitted sequence) or one of the target residues (equivalent to containing proposed mutation), respectively.
  • Residues that exist as one of the target residues (A) in aligned sequence are shown in blue and have a positive contribution to the analysis score.
  • Conserved residues are shown in red and have a negative impact on the analysis score.