PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL

BMC Bioinformatics

Research

Stefano Pascarella¹  Alessandro Paiardini¹  Emanuele Bramucci¹  Francesco Bossa¹ 

[1] Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185, Roma, Italy;

关键词: Structural Alignment;    Modeling Task;    Protein Structure Prediction;    Multiple Structural Alignment;    Multiple Sequence Alignment Tool;   

DOI  :  10.1186/1471-2105-13-S4-S2

来源: Springer

【 摘 要 】

BackgroundIn recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users.ResultsA simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models.ConclusionsPyMod represents a new tool for the analysis and the manipulation of protein sequences and structures. The ease of use, integration with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, are the key features of this tool.Source code, installation instructions, video tutorials and a user's guide are freely available at the URL http://schubert.bio.uniroma1.it/pymod/index.html

【 授权许可】

Unknown   
© Bramucci et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.