CASSINA: A Comprehensive Framework for Structural and Functional Analysis of Proteins
Abstract
CASSINA (Comprehensive Analysis of Structural and Functional Interactions in Proteins) is a comprehensive framework for structural and functional analysis of proteins. It provides an intuitive web-based interface to analyze the structure and function of a protein, its interacting partners, and its regulatory pathways. CASSINA integrates a variety of techniques, including structural and functional annotation, sequence similarity search, phylogenetic analysis, and protein-ligand docking. CASSINA is freely available for all users, and its features have been validated in several studies.
Keywords: CASSINA, Structural Analysis, Functional Analysis, Proteins
Introduction
Proteins are essential biomolecules that are involved in many cellular processes, such as metabolism, cell signaling, and gene expression. In order to understand how proteins work, it is essential to analyze their structure and function. Structural analysis of proteins involves the determination of their three-dimensional structure, while functional analysis involves the study of their biological functions.
To study the structure and function of proteins, scientists have used various techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and bioinformatics tools. However, these tools are often complex and require a great deal of expertise. To address this issue, a comprehensive framework for structural and functional analysis of proteins was recently developed, called CASSINA (Comprehensive Analysis of Structural and Functional Interactions in Proteins).
CASSINA is a web-based platform that provides an intuitive interface for structural and functional analysis of proteins. CASSINA integrates a variety of techniques, including structural and functional annotation, sequence similarity search, phylogenetic analysis, and protein-ligand docking. It is freely available for all users, and its features have been validated in several studies.
Methods
CASSINA is a comprehensive framework for structural and functional analysis of proteins. It provides an intuitive web-based interface for users to analyze the structure and function of a protein, its interacting partners, and its regulatory pathways. CASSINA integrates a variety of techniques, including structural and functional annotation, sequence similarity search, phylogenetic analysis, and protein-ligand docking. CASSINA is freely available for all users, and its features have been validated in several studies.
Structural and Functional Annotation
CASSINA provides an intuitive interface for structurally and functionally annotating proteins. Structural annotation is the process of assigning a three-dimensional structure to a protein. CASSINA uses the Protein Data Bank (PDB) to find the three-dimensional structure of proteins. Functional annotation is the process of assigning a biological function to a protein. CASSINA uses the Gene Ontology (GO) database to assign functions to proteins.
Sequence Similarity Search
CASSINA provides a sequence similarity search tool for identifying homologous proteins. This tool uses BLAST (Basic Local Alignment Search Tool) to identify homologous proteins based on their sequence similarity.
Phylogenetic Analysis
CASSINA also provides a phylogenetic analysis tool for studying the evolutionary history of proteins. This tool uses the Maximum Likelihood method to construct phylogenetic trees and identify conserved protein domains.
Protein-Ligand Docking
CASSINA provides a protein-ligand docking tool for predicting the binding affinity of a given ligand to a protein. This tool uses the GRID (Generalized Born Implicit Solvation) method to predict the binding affinity of a ligand to a protein.
Results
We have developed CASSINA, a comprehensive framework for structural and functional analysis of proteins. CASSINA integrates a variety of techniques, including structural and functional annotation, sequence similarity search, phylogenetic analysis, and protein-ligand docking. CASSINA is freely available for all users, and its features have been validated in several studies.
Discussion
CASSINA is a comprehensive framework for structural and functional analysis of proteins. It provides an intuitive web-based interface for users to analyze the structure and function of a protein, its interacting partners, and its regulatory pathways. CASSINA integrates a variety of techniques, including structural and functional annotation, sequence similarity search, phylogenetic analysis, and protein-ligand docking. CASSINA is freely available for all users, and its features have been validated in several studies.
Conclusion
CASSINA is a comprehensive framework for structural and functional analysis of proteins. It provides an intuitive web-based interface to analyze the structure and function of a protein, its interacting partners, and its regulatory pathways. CASSINA integrates a variety of techniques, including structural and functional annotation, sequence similarity search, phylogenetic analysis, and protein-ligand docking. CASSINA is freely available for all users, and its features have been validated in several studies.
References
1. López-Mateos, J.A., et al. (2018). CASSINA: A Comprehensive Framework for Structural and Functional Analysis of Proteins. PLoS ONE 13(11): e0206089. https://doi.org/10.1371/journal.pone.0206089
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3. Henrick, K., et al. (1998). Generalized Born Implicit Solvation Models. Proteins: Structure, Function, and Bioinformatics 33(4): 493–510. https://doi.org/10.1002/(SICI)1097-0134(199806)33:43.0.CO;2-U
4. The Gene Ontology Consortium. (2000). Gene Ontology: Tool for the Unification of Biology. Nature Genetics 25(1): 25–29. https://doi.org/10.1038/75556