Development and Application of Novel ... - Jacobs University

PART I: CAPDE
library. The challenges and advances to generate the functionally diverse libraries have
been reviewed in past year.[20,26] Computational tools can assist directed evolution in
these two steps by in-silico analysis and screening of expected protein sequence space
sampled by generated libraries (summarized in Table 1.1). Publicly available web servers,
MAP (Mutagenesis Assistant Program)[25,27] and PEDAL-AA[28] were developed to
estimate the diversity at protein level in the library generated by random mutagenesis
method.
Table 1.1: Summarizing computational tools to analyze amino acid diversity, size and
completeness of the library generated by mutagenesis methods.
Approach Name Input
Nucleotide
MAP 2.0 3D
sequence or
[25,27]
protein structure.
Statistics of
Nucleotide
generated
sequence,
diversity
PEDEL-AA mutation rate,
[28] library size, indel
rate, nucleotide
mutation matrix.
Library size and
Library size GLUE-IT
randomization
and
[28]
techniques.
completenes
s
Probability
TopLib [30]
required by
Case study
examples
Cytochrome
P450BM-3,[25] D-
amino acid oxidase,
Phytase [27]
α-synuclein,
Phosphoribosylpyro
phosphate
amidotransferase
(purF) [29]
Randomization
scheme: NNK. NDT,
NNB, NAY [28]
Randomization
scheme: NNN, NNB,
URL
http://map.jacob
s-
university.de/su
bmission.html
http://guinevere
.otago.ac.nz/cgi-
bin/aef/pedel-
AA.pl
http://guinevere
.otago.ac.nz/cgi-
bin/aef/glue-
IT.pl
http://stat.haifa.
ac.il/~yuval/topl
6