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Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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.

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Related Experiment Video

Updated: May 21, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics,

Yao Chi Chen¹, Jon D Wright, Carmay Lim

¹Institute of Biomedical Sciences, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.

Nucleic Acids Research

|June 5, 2012

Summary

DR_bind is a novel web server that predicts DNA-binding residues using electrostatics, evolution, and geometry. This method bypasses the need for training data, offering accurate predictions for novel protein structures.

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Last Updated: May 21, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

Analyzing and Building Nucleic Acid Structures with 3DNA

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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:

Identifying DNA-binding residues is crucial for understanding gene regulation and protein function.
Existing computational methods often rely on large training datasets or specific parameters.

Purpose of the Study:

To develop and present DR_bind, a web server for automated prediction of DNA-binding residues.
To offer a parameter-free, training-data-independent approach for DNA-binding residue prediction.

Main Methods:

DR_bind analyzes protein structures (PDB format) using electrostatics, evolutionary conservation, and geometric features.
It identifies conserved, solvent-accessible residues stabilized electrostatically upon mutation.
The server does not require a training dataset or machine learning algorithms.

Main Results:

The server achieved high prediction accuracy (90%) and precision (47%) on DNA-bound structures.
It also demonstrated strong performance on DNA-free structures with 88% accuracy and 42% precision.
DR_bind provides downloadable results, including residue lists and 3D visualizations.

Conclusions:

DR_bind offers a robust and accessible tool for predicting DNA-binding residues without prior training data.
Its ability to predict residues in novel structures is valuable for structural genomics projects.
The web server is freely available, facilitating broader research applications.