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RELATED
LINKS
Links to some useful and user-friendly
websites for improving randomized library design and analyzing library diversity. Most of the sites listed below are
discussed further in:
Patrick, W.M. and Firth, A.E.
Strategies and computational tools for improving randomized
protein libraries.
Biomol. Eng. 2005; 22, 105-112.
1. Structure-guided evolution
ConSurf and ConSurf-HSSP
Assess evolutionary conservation at each amino acid position of a target protein and project it onto the 3-D structure. ConSurf generates
its own multiple sequence alignments (MSAs) to calculate residue conservation, while ConSurf-HSSP uses the pre-calculated MSAs of the HSSP database.
Web servers: ConSurf; ConSurf-HSSP
SCHEMA
Scans a known 3-D structure for local networks of interactions, and therefore identifies putative crossover
points.
Web server: http://www.mayo.caltech.edu/~pcs/initialschemapage.html
2. Estimating library completeness and diversity
GLUE, PEDEL and DRIVeR
A suite of programs for estimating the completeness and diversity in libraries generated by error-prone PCR, DNA
shuffling, StEP PCR, saturation mutagenesis, synthetic shuffling, etc. The web interface also calculates and plots
variables associated with library design, such as optimal mutation rates and target library sizes.
Web server and source code: http://guinevere.otago.ac.nz/stats.html
3. Other useful sites
ESPSearch
Donald Doyle's search tool for locating exact sequences and patterns of any length in any source sequence. Like BLAST, only better!
Source code: http://web.chemistry.gatech.edu/~doyle/espsearch
Dali
Find the structural neighbours of any given protein in the PDB.
Web server: http://www.ebi.ac.uk/dali
X-factor calculator
Use sequencing data from error-prone PCR libraries to estimate the robustness of your protein in the face of random mutation.
Web server: http://depts.washington.edu/loeblabs/protocols/xfactor.htm
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