Development and Application of Novel ... - Jacobs University
Development and Application of Novel ... - Jacobs University
Development and Application of Novel ... - Jacobs University
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PART I: CAPDE<br />
protein <strong>and</strong> facilitates in-<br />
silico alanine screening,<br />
mutant homology<br />
modeling <strong>and</strong><br />
interaction energy<br />
calculation.<br />
The program suite<br />
PEAT-SA [118]<br />
predict mutational effect<br />
on protein stability,<br />
lig<strong>and</strong> affinity <strong>and</strong> pKa<br />
http://enzyme.ucd.ie/PEA<br />
TSA/Pages/FrontPage.php<br />
values.<br />
The web server predicts<br />
CUPSAT [119]<br />
mutational effect on<br />
http://cupsat.tu-bs.de/<br />
protein stability.<br />
The web server predicts<br />
RF, SVM, Tree<br />
<strong>and</strong> SVM<br />
regression<br />
AUTO-MUTE<br />
[121]<br />
mutational effect on<br />
protein stability <strong>and</strong><br />
activity (up to 19<br />
http://proteins.gmu.edu/a<br />
utomute/<br />
mutations).<br />
Evolutionary<br />
conservation<br />
SIFT [122]<br />
The web server predicts<br />
mutational effect on<br />
protein function.<br />
http://sift.jcvi.org/<br />
1.7. Summary <strong>and</strong> outlook<br />
In this chapter, the recent additions to the CAPDE arsenal <strong>of</strong> computational tools,<br />
servers <strong>and</strong> databases have been briefly reviewed. The rapid accumulation <strong>of</strong> the<br />
knowledge on protein structures <strong>and</strong> sequence-structure-function relationships foresee<br />
the continuous amelioration <strong>of</strong> these methods. In particular, machine-learning approaches,<br />
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