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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL
Emanuele Bramucci1, Alessandro Paiardini, Francesco Bossa
1Dipartimento di Scienze Biochimiche A, Rossi Fanelli, Sapienza Università di Roma, Roma 00185, Italy.
BMC Bioinformatics
|April 28, 2012
Summary
PyMod simplifies protein analysis and homology modeling by integrating multiple tools within the PyMOL framework. This user-friendly interface reduces the learning curve for complex sequence and structure manipulation tasks.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Numerous open-source tools exist for protein sequence analysis, editing, and modeling.
- Steep learning curves of existing tools hinder adoption by researchers.
Purpose of the Study:
- To develop an integrated and user-friendly interface for protein sequence and structure analysis.
- To simplify homology modeling and related tasks by leveraging existing powerful tools.
Main Methods:
- Developed PyMod, an interface connecting PyMOL with tools like PSI-BLAST, ClustalW, MUSCLE, CEalign, and MODELLER.
- Integrated functionalities for sequence similarity searches, multiple sequence and structural alignment generation/editing.
- Enabled merging of sequence and structure alignments within the PyMOL environment.
Main Results:
- PyMod offers a simplified workflow for complex protein analysis and homology modeling.
- The tool integrates sequence similarity searches, alignment generation, and editing.
- Users can perform advanced sequence and structure manipulation within a single framework.
Conclusions:
- PyMod enhances protein sequence and structure analysis and manipulation.
- Key features include ease of use and integration with popular tools like PyMOL.
- Freely available resources include source code, tutorials, and a user's guide.
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