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 Ramos
Regular Article
Part of the following topical collections:
  1. Nascimento Festschrift Collection

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.

Keywords

Protein–protein interactions Amber VMD MMPBSA Software 

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
  1. 1.REQUIMTE, Departamento de Química e Bioquímica, Faculdade de CiênciasUniversidade do PortoPortoPortugal

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