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Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Protein Organization

Protein Organization

Protein Organization

Protein Organization

Protein Organization

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Nucleic Acid Structure

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

ArchDB 2014: structural classification of loops in proteins.

Jaume Bonet¹, Joan Planas-Iglesias, Javier Garcia-Garcia

¹Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB), Barcelona, Catalonia, 08950, Spain and Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA Aberystwyth, Ceredigion, UK.

Nucleic Acids Research

|November 23, 2013

Summary

The ArchDB database now offers an updated, user-friendly platform for classifying protein loops. This resource aids in understanding protein structure, function, and design through advanced computational methods.

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Protein function is dictated by its 3D structure, comprising regular elements (β-strands, α-helices) and variable loops.
Protein loops are crucial for protein function, folding, and dynamics, yet their variability poses classification challenges.
Accurate classification of protein loops is vital for homology modeling, structure prediction, and protein design.

Purpose of the Study:

To present a completely reworked and updated version of the ArchDB database.
To provide a novel, efficient, and user-friendly resource for the structural classification of protein loops.
To enhance applications in protein structure prediction, design, and function prediction.

Main Methods:

Development of a novel, fast, and user-friendly web-based interface for ArchDB.
Implementation of a novel graph-based, computationally efficient clustering algorithm.
Classification of a large dataset of protein loops.

Main Results:

The updated ArchDB classifies 149,134 protein loops.
These loops are organized into 5739 distinct classes and 9608 subclasses.
The new version offers improved accessibility and computational efficiency.

Conclusions:

The enhanced ArchDB provides a valuable resource for structural biologists and bioinformaticians.
The novel classification methods improve the understanding of protein loop structures and their functional implications.
This updated database supports advancements in protein structure prediction, design, and function prediction.