2014 | OriginalPaper | Buchkapitel
CompASM: an Amber-VMD alanine scanning mutagenesis plug-in
verfasst von : João V. Ribeiro, Nuno M. F. S. A. Cerqueira, Irina S. Moreira, Pedro A. Fernandes, Maria João Ramos
Erschienen in: Marco Antonio Chaer Nascimento
Verlag: Springer Berlin Heidelberg
Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.
Wählen Sie Textabschnitte aus um mit Künstlicher Intelligenz passenden Patente zu finden. powered by
Markieren Sie Textabschnitte, um KI-gestützt weitere passende Inhalte zu finden. powered by
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.