Theoretical Chemistry Accounts

, 131:1271 | Cite as

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

  • João V. Ribeiro
  • Nuno M. F. S. A. Cerqueira
  • Irina S. Moreira
  • Pedro A. Fernandes
  • Maria João RamosEmail author
Regular Article
Part of the following topical collections:
  1. Nascimento Festschrift Collection


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


Protein–protein interactions Amber VMD MMPBSA Software 



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).

Supplementary material

214_2012_1271_MOESM1_ESM.pdf (917 kb)
Supplementary material 1 (PDF 916 kb)


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • João V. Ribeiro
    • 1
  • Nuno M. F. S. A. Cerqueira
    • 1
  • Irina S. Moreira
    • 1
  • Pedro A. Fernandes
    • 1
  • Maria João Ramos
    • 1
    Email author
  1. 1.REQUIMTE, Departamento de Química e Bioquímica, Faculdade de CiênciasUniversidade do PortoPortoPortugal

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