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

• Type: Article in International Scientific Journal
• Date: 2012

Authors

Joao V Ribeiro (Author) Other; Nuno M F S A Cerqueira (Author) FCUP; Irina S Moreira (Author) Other; Pedro A Fernandes (Author) FCUP; Maria Joao Ramos (Author) FCUP

Journal

Title: Theoretical Chemistry Accounts

Vol. 131 No. 3

Pages: 1-7

ISSN: 1432-881X

Publisher: Springer Nature

Indexing

ISI Web of Knowledge - 11 Citations

Scopus - 13 Citations

Scientific classification

FOS: Natural sciences > Chemical sciences

Other information

Authenticus ID: P-002-4Y5

DOI: 10.1007/s00214-012-1271-2

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 7