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

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.

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Acknowledgments

The authors would like to thank the FCT (Fundação para a Ciência e Tecnologia) for financial support (Grants SFRH/BD/61324/2009 and PTDC/QUI-QUI/103118/2008).

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Correspondence to Maria João Ramos.

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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. et al. CompASM: an Amber-VMD alanine scanning mutagenesis plug-in. Theor Chem Acc 131, 1271 (2012). https://doi.org/10.1007/s00214-012-1271-2

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Keywords

  • Protein–protein interactions
  • Amber
  • VMD
  • MMPBSA
  • Software