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CompASM: an Amber-VMD alanine scanning mutagenesis plug-in

Title
CompASM: an Amber-VMD alanine scanning mutagenesis plug-in
Type
Article in International Scientific Journal
Year
2012
Authors
Joao V Ribeiro
(Author)
Other
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Irina S Moreira
(Author)
Other
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Maria Joao Ramos
(Author)
FCUP
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Journal
Vol. 131 No. 3
Pages: 1-7
ISSN: 1432-881X
Publisher: Springer Nature
Scientific classification
FOS: Natural sciences > Chemical sciences
Other information
Authenticus ID: P-002-4Y5
Abstract (EN): Alanine scanning mutagenesis (ASM) of protein-protein interfacial residues is a popular means to understand the structural and energetic characteristics of hot spots in protein complexes. In this work, we present a computational approach that allows performing such type of analysis based on the molecular mechanics/Poisson-Boltzmann surface area method. This computational approach has been used largely in the past and has proven to give reliable results in a wide range of complexes. However, the sequential preparation and manual submission of dozens of files has been often a major obstacle in using it. To overcome these limitations and turn this approach user-friendly, we have designed the plug-in CompASM (computational alanine scanning mutagenesis). This software has an easy-to-use graphical interface to prepare the input files, run the calculations, and analyze the final results. CompASM was built in TCL/TK programming language to be included in VMD as a plug-in. The CompASM package is distributed as an independent platform, with script code under the GNU Public License from http://compbiochem.org/Software/compasm/Home.html.
Language: English
Type (Professor's evaluation): Scientific
Contact: mjramos@fc.up.pt
No. of pages: 7
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