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

Mass Spectrometry: Molecular Fragmentation Overview

Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Lagging Strand Synthesis

Lagging Strand Synthesis

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Source Transformation

Source Transformation

Source transformation is a fundamental technique employed in circuit analysis, offering a valuable tool for simplifying complex electrical circuits. This technique involves the replacement of either a voltage source in series with a resistor by a current source in parallel with a resistor, or vice versa. The key concept here is that when the original sources are deactivated (turned off), the equivalent resistance at the circuit's end terminals remains the same.
It is essential to note that when...

RACE - Rapid Amplification of cDNA Ends

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...

You might also read

Related Articles

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

Sort by

Same author

Correction: Relative telomere length and senescence-associated inflammatory cytokines as blood-based prognostic markers in patients with advanced or resectable gastro-oesophageal adenocarcinoma.

British journal of cancer·2025

Same author

Relative telomere length and senescence-associated inflammatory cytokines as blood-based prognostic markers in patients with advanced or resectable gastro-oesophageal adenocarcinoma.

British journal of cancer·2025

Same author

Reversible Small Molecule Multivariant Ras Inhibitors Display Tunable Affinity for the Active and Inactive Forms of Ras.

Journal of medicinal chemistry·2025

Same author

Fragment-based drug discovery-the importance of high-quality molecule libraries.

Molecular oncology·2022

Same author

Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling.

Journal of medicinal chemistry·2022

Same author

Automated Generation of Novel Fragments Using Screening Data, a Dual SMILES Autoencoder, Transfer Learning and Syntax Correction.

Journal of chemical information and modeling·2021

Search research articles

Related Experiment Video

Updated: Aug 23, 2025

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Implementation of an AI-assisted fragment-generator in an open-source platform.

Alan E Bilsland¹, Angelo Pugliese², Justin Bower¹

¹Cancer Research Horizons - Therapeutic Innovation, Cancer Research UK Beatson Institute Garscube Estate, Switchback Road Glasgow G61 1BD UK.

RSC Medicinal Chemistry

|November 2, 2022

Summary

A new deep learning model for fragment library design is now available in KNIME, making hit identification more accessible to researchers without extensive programming skills.

More Related Videos

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

A Customizable Protocol for String Assembly gRNA Cloning STAgR

A Customizable Protocol for String Assembly gRNA Cloning STAgR

Published on: December 26, 2018

Related Experiment Videos

Last Updated: Aug 23, 2025

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

A Customizable Protocol for String Assembly gRNA Cloning STAgR

A Customizable Protocol for String Assembly gRNA Cloning STAgR

Published on: December 26, 2018

Area of Science:

Computational chemistry
Drug discovery
Bioinformatics

Background:

Fragment library design is crucial for efficient hit identification in drug discovery.
Previous deep learning models for this task were limited to users with Python programming expertise.

Purpose of the Study:

To develop a user-friendly implementation of a deep learning model for fragment library design.
To enable researchers with limited programming knowledge to utilize advanced computational tools.

Main Methods:

The study involved adapting a previously developed Python-based deep learning model.
The model was reimplemented within the KNIME graphical pipelining environment.
KNIME allows for visual workflow construction, simplifying model usage.

Main Results:

A functional KNIME workflow for deep learning-based fragment library design has been created.
This implementation lowers the barrier to entry for utilizing sophisticated drug discovery tools.
The model facilitates the design of fragment libraries for efficient hit identification.

Conclusions:

The KNIME implementation democratizes access to advanced fragment library design tools.
This advancement is expected to accelerate hit identification processes in drug discovery.
Researchers can now leverage deep learning for fragment-based drug design without coding expertise.