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Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision
Mohamed Machat1, Florent Langenfeld1, Daniela Craciun1
1Laboratoire GBCM, EA 7528, Conservatoire National des Arts et Métiers, Hesam Université, Paris 75003, France.
Bioinformatics (Oxford, England)
|July 11, 2021
Summary
Computer vision shape retrieval methods can effectively analyze protein structures. These methods help identify protein similarities and potential interactions by focusing on surface geometry, advancing structure-function understanding.
Area of Science:
- Structural biology
- Bioinformatics
- Computational chemistry
Background:
- Molecular structure and surface geometry are crucial for biomolecular interactions and functions.
- Understanding protein shapes aids in predicting molecular recognition events.
- Existing methods for analyzing protein structures can be enhanced by geometric approaches.
Purpose of the Study:
- To evaluate the efficacy of shape retrieval techniques from computer vision for analyzing protein structures.
- To explore the potential of protein surface shape as a high-level structural representation.
- To demonstrate the utility of shape retrieval for identifying homologous proteins and interaction partners.
Main Methods:
- Application of reference shape retrieval methods, commonly used in computer vision, to protein structures.
- Analysis of protein surface geometry as a descriptor for structural and functional properties.
- Screening of large protein structure databases using shape retrieval algorithms.
Main Results:
- Shape retrieval methods demonstrate efficiency in identifying orthologous proteins.
- These methods are effective in tracking significant conformational changes in proteins.
- Protein surface shape analysis facilitates the identification of surficial homologs and potential interacting partners.
Conclusions:
- Protein surface shape offers a valuable, abstract representation of protein structure, independent of sequence or fold.
- Shape retrieval techniques provide a powerful tool for large-scale screening of protein structure databases.
- This approach extends the traditional structure-function paradigm to a structure-surface(s)-function paradigm, opening new avenues in biological research.
