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iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach.
Guilhem Faure1, Agnel Praveen Joseph1,2,3,4, Pierrick Craveur1,2,3,5
1INSERM, U 1134, DSIMB, Univ Paris, Univ de la Réunion, Univ des Antilles, F-75739 Paris, France.
Source Code for Biology and Medicine
|November 9, 2019
Summary
This study introduces iPBAvizu, a PyMOL plugin for protein structure superimposition analysis. It enhances protein structure comparison using a Structural Alphabet approach, improving accuracy and user-friendliness for evolutionary and functional insights.
Area of Science:
- Structural biology
- Bioinformatics
- Computational biology
Background:
- Protein 3D structure dictates function, making structural comparison essential for understanding evolution and function.
- Existing methods often rely on sequence alignment, neglecting crucial structural features.
- Structural Alphabet (SA) provides a method to represent 3D protein structures as 1D sequences.
Purpose of the Study:
- To develop an improved protein structure superimposition method.
- To create a user-friendly tool for analyzing protein structural alignments.
Main Methods:
- Utilized Protein Blocks (PB), a Structural Alphabet with 16 prototypes representing pentapeptide conformations.
- Developed an improved sequence alignment procedure based on dynamic programming and a dedicated PB Substitution Matrix.
- Implemented a two-step search strategy: high-weight alignment of similar regions followed by completion with less stringent parameters (iPBA).
Main Results:
- The iPBA approach demonstrated superior performance compared to existing tools in benchmark tests.
- Developed iPBAvizu, a PyMOL plugin to facilitate the use of iPBA.
- iPBAvizu enables easy execution of iPBA and interactive analysis of protein superimpositions.
Conclusions:
- iPBAvizu integrates the iPBA method into the PyMOL software.
- The plugin allows users to generate iPBA alignments and explore structural superimpositions interactively.
- iPBAvizu aids in assessing the quality of protein structural alignments.
Keywords:
Protein superimpositionStructural alignmentStructural alphabetStructural bioinformaticsVisualisationMore Related Videos
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