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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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DNA Helicases00:55

DNA Helicases

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DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
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Related Experiment Video

Updated: Jan 30, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

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DBSI server: DNA binding site identifier.

Shravan Sukumar1, Xiaolei Zhu2, Spencer S Ericksen3

  • 1Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

Bioinformatics (Oxford, England)
|June 5, 2016
PubMed
Summary
This summary is machine-generated.

Identifying DNA binding sites on proteins is crucial for understanding cellular events. The DNA Binding Site Identifier (DBSI) webserver uses a structure-based model to accurately predict these sites on protein surfaces.

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Area of Science:

  • Structural biology
  • Computational biology
  • Molecular interactions

Background:

  • Protein-nucleic acid interactions are vital for regulating cellular processes.
  • Predicting DNA binding sites from protein structure alone presents a significant challenge.

Purpose of the Study:

  • To introduce the webserver interface for the DNA Binding Site Identifier (DBSI).
  • To provide a tool for predicting and visualizing DNA binding sites on protein structures.

Main Methods:

  • Utilizing a structure-based Support Vector Machine (SVM) model.
  • Developing a webserver for user-friendly access to the DBSI model.

Main Results:

  • DBSI demonstrates top performance in predicting DNA binding sites on protein and peptide surfaces.
  • The model shows potential for predicting RNA binding sites.

Conclusions:

  • DBSI offers a powerful and accurate method for identifying DNA binding sites from protein structures.
  • The webserver facilitates the study of protein-DNA interactions in molecular biology research.