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Related Concept Videos

Protein Organization01:24

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 Organization01:13

Protein Organization

Overview
Protein-protein Interfaces02:04

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...
Conserved Binding Sites01:49

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 Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

PiDNA: Predicting protein-DNA interactions with structural models.

Chih-Kang Lin1, Chien-Yu Chen

  • 1Center for Systems Biology, National Taiwan University, Taipei 106, Taiwan.

Nucleic Acids Research
|May 25, 2013
PubMed
Summary
This summary is machine-generated.

PiDNA predicts transcription factor binding sites using structural models and knowledge-based scoring. This tool generates accurate position weight matrices (PWMs) for understanding gene regulation and designing experiments.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

  • Computational Biology
  • Structural Biology
  • Genomics

Background:

  • Predicting transcription factor binding sites is crucial for gene regulation but remains challenging.
  • Protein Data Bank structures offer insights into protein-DNA interactions.
  • Physics-based and knowledge-based potentials can derive position weight matrices (PWMs) from structural data.

Purpose of the Study:

  • To develop PiDNA, a web server for constructing reliable PWMs from in silico mutated protein-DNA complex structures.
  • To predict protein-DNA interactions using PWMs derived from structural models with minimal energy changes.
  • To enable users to predict sequence preferences and obtain structural models.

Main Methods:

  • Utilized an atomic-level knowledge-based scoring function on in silico mutated complex structures.
  • Constructed PWMs from favorable mutated structures with small energy changes.
  • Predicted relative DNA sequence preferences for limited and unlimited mutations.

Main Results:

  • Constructed PWMs demonstrated similarity to experimentally annotated PWMs.
  • PiDNA accurately identified high-specificity binding sites when compared against protein-binding microarray data.
  • The tool successfully distinguished validated binding sites from random sequences with high accuracy.

Conclusions:

  • PiDNA provides a valuable tool for predicting transcription factor binding preferences and designing biological experiments.
  • The server facilitates the request of mutated structure models for protein design.
  • PiDNA has the potential to enhance in vivo protein-DNA interaction inference when integrated with chromatin immunoprecipitation data.