Abstract
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.
Electronic supplementary material The online version of this article (doi:10.1007/s00214-012-1271-2) contains supplementary material, which is available to authorized users.
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Dedicated to Professor Marco Antonio Chaer Nascimento and published as part of the special collection of articles celebrating his 65th birthday.
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Ribeiro, J.V., Cerqueira, N.M.F.S.A., Moreira, I.S., Fernandes, P.A., Ramos, M.J. (2014). CompASM: an Amber-VMD alanine scanning mutagenesis plug-in. In: Ornellas, F., João Ramos, M. (eds) Marco Antonio Chaer Nascimento. Highlights in Theoretical Chemistry, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-41163-2_8
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DOI: https://doi.org/10.1007/978-3-642-41163-2_8
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