Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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...

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

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...

Single-Strand DNA Binding Proteins

Single-Strand DNA Binding Proteins

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...

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...

Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

RGTBind: RBF-gate graph transformer with spatially biased attention for protein-DNA binding-site prediction.

Journal of molecular modeling·2026

Same author

Chimeric antigen receptor-T cell therapy-induced cardiotoxicity: Pathophysiological mechanisms and pharmacological intervention strategies.

Pharmacological research·2026

Same author

Targeting AVEN Liquid-Liquid Phase Separation in Colorectal Cancer: Insights From a Raddeanin A-Based Chemical Probe.

Basic & clinical pharmacology & toxicology·2026

Same author

Efficacy and Safety of Fibroblast Activation Protein Targeted Radioligand Therapy for Advanced Solid Tumour: A Systematic Review and Meta-Analysis.

Dose-response : a publication of International Hormesis Society·2026

Same author

Transthyretin V122I variant and protein affect cardiac severity and mortality in sickle cell disease.

Blood advances·2026

Same author

Variations in mitochondrial genome as potential prognostic markers in sickle cell disease.

Haematologica·2026

Same journal

Modeling the impact of budget limitation on the screening and treatment pathway of HPV-induced precancerous cervical lesions.

Mathematical biosciences and engineering : MBE·2026

Same journal

Modeling the effects of trait-mediated dispersal on coexistence of two species: Competition and non-consumptive predator-prey.

Mathematical biosciences and engineering : MBE·2026

Same journal

A close look at the viral reduction rate in target cell limited models.

Mathematical biosciences and engineering : MBE·2026

Same journal

A stochastic agent-based model for simulating tumor-immune dynamics and evaluating therapeutic strategies.

Mathematical biosciences and engineering : MBE·2026

Same journal

Addressing domain shift via imbalance-aware domain adaptation in embryo development assessment.

Mathematical biosciences and engineering : MBE·2026

Same journal

Effect of drug resistance on an HIV epidemic in heterogeneous populations.

Mathematical biosciences and engineering : MBE·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Sep 5, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

DNA-binding protein prediction based on deep transfer learning.

Jun Yan¹, Tengsheng Jiang¹, Junkai Liu¹

¹College of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China.

Mathematical Biosciences and Engineering : MBE

|July 8, 2022

Summary

This summary is machine-generated.

This study introduces a novel transfer learning approach for predicting DNA binding proteins (DBPs). By leveraging transfer learning and deep learning with attention mechanisms, it enhances DBP detection efficiency.

Keywords:

DNA-Binding protein deep learning transfer learning

More Related Videos

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data

A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data

Published on: September 25, 2021

Related Experiment Videos

Last Updated: Sep 5, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data

A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data

Published on: September 25, 2021

Area of Science:

Biochemistry and Molecular Biology
Bioinformatics
Computational Biology

Background:

DNA binding proteins (DBPs) are crucial in biomedical research, necessitating accurate prediction methods.
Traditional machine learning for DBP prediction is resource-intensive.
Transfer learning offers a promising alternative for efficient DBP detection.

Purpose of the Study:

To develop an efficient method for predicting DNA binding proteins (DBPs).
To explore the utility of transfer learning in DBP prediction.
To compare classical transfer learning algorithms for dataset construction.

Main Methods:

Feature extraction from protein sequences.
Application of transfer learning with two classical algorithms.
Construction of datasets using transferred samples.
Development of a deep learning neural network model incorporating attention mechanisms for DBP detection.

Main Results:

Demonstrated the effectiveness of transfer learning in DBP prediction.
Identified optimal transfer learning strategies for dataset construction.
Achieved accurate DBP detection using a deep learning model with attention.

Conclusions:

Transfer learning significantly improves the efficiency of DBP prediction.
Deep learning models with attention mechanisms are effective for DBP detection.
The proposed method reduces the need for extensive human effort and resources in DBP prediction.