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

VSEPR Theory

VSEPR Theory

Valence shell electron-pair repulsion theory (VSEPR theory) enables us to predict the molecular structure around a central atom from an examination of the number of bonds and lone electron pairs in its Lewis structure. The VSEPR model assumes that electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between these electron pairs by maximizing the distance between them. The electrons in the valence shell of a central atom form either bonding...

You might also read

Related Articles

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

Sort by

Same journal

CNV-ECOD: A copy number variation detection method based on ECOD algorithm using next-generation sequencing data.

Journal of bioinformatics and computational biology·2026

Same journal

ReinVar: A model-free paradigm-based reinforcement learning approach to detect copy number variation.

Journal of bioinformatics and computational biology·2026

Same journal

When pipelines run but coordinates fail: A simple spatial specificity check for false locality in post-GWAS analysis.

Journal of bioinformatics and computational biology·2026

Same journal

Comparative benchmarking of template-based, evolutionary-diffusion, and generative language models for IsPETase structure prediction.

Journal of bioinformatics and computational biology·2026

Same journal

Trap spaces as labelled ideals of SCC posets: A structural-functional theory of reachability in asynchronous boolean networks.

Journal of bioinformatics and computational biology·2026

Same journal

Erratum - DDINet: Drug-drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder.

Journal of bioinformatics and computational biology·2026

Search research articles

Related Experiment Video

Updated: May 3, 2026

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

Visual-SELEX: A technology ensemble for evaluating aptamer structural similarity via 3D visual spatial conformational

¹Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China.

Journal of Bioinformatics and Computational Biology

|August 14, 2025

Summary

This study introduces Visual-SELEX, a program evaluating three-dimensional (3D) structural similarity in single-stranded DNA (ssDNA). It reveals 3D structural consistency is crucial, offering insights beyond traditional sequence-based comparisons.

Keywords:

3D point cloud Aptamer structure structural similarity visual analysis

More Related Videos

Analysis of SEC-SAXS data via EFA deconvolution and Scatter

Analysis of SEC-SAXS data via EFA deconvolution and Scatter

Published on: January 28, 2021

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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

Related Experiment Videos

Last Updated: May 3, 2026

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

Analysis of SEC-SAXS data via EFA deconvolution and Scatter

Analysis of SEC-SAXS data via EFA deconvolution and Scatter

Published on: January 28, 2021

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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:

Biochemistry
Computational Biology
Structural Biology

Background:

Traditional single-stranded DNA (ssDNA) similarity studies focus on base sequence identity.
One-dimensional sequence analysis has limitations in capturing the three-dimensional (3D) structural consistency of ssDNA aptamers.
Accurate evaluation of 3D spatial consistency in ssDNA is necessary for advanced applications.

Purpose of the Study:

To develop a program for rapid and accurate evaluation of 3D spatial consistency of ssDNA.
To address the limitations of sequence-only similarity assessments in nucleic acid aptamer studies.

Main Methods:

Designed the Visual-SELEX program for analyzing ssDNA sequence sets.
Employed coarse-grained and molecular dynamics (MD) simulations to generate stable 3D ssDNA structures.
Converted 3D structures into point cloud models for alignment and superposition analysis.

Main Results:

Visual-SELEX successfully generated 3D structures of ssDNA from enriched sequences.
The program accurately matched ssDNAs with dissimilar base sequences but similar 3D structures.
Demonstrated that 3D spatial similarity analysis provides richer information than sequence similarity alone.

Conclusions:

Visual-SELEX offers a novel approach to assess ssDNA structural similarity in three dimensions.
The findings highlight the importance of considering 3D structure for aptamer design and function.
This method enhances the understanding of ssDNA aptamer behavior and interactions.