Related Experiment Video

Updated: Aug 23, 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

DHU-Pred: accurate prediction of dihydrouridine sites using position and composition variant features on diverse

Muhammad Taseer Suleman¹, Tamim Alkhalifah², Fahad Alturise²

¹Department of Computer Science, School of Systems and Technology, University of Management & Technology, Lahore, Pakistan.

|November 2, 2022

Abstract

Background:

Dihydrouridine (D) is a modified transfer RNA post-transcriptional modification (PTM) that occurs abundantly in bacteria, eukaryotes, and archaea. The D modification assists in the stability and conformational flexibility of tRNA. The D modification is also responsible for pulmonary carcinogenesis in humans.

Objective:

For the detection of D sites, mass spectrometry and site-directed mutagenesis have been developed. However, both are labor-intensive and time-consuming methods. The availability of sequence data has provided the opportunity to build computational models for enhancing the identification of D sites. Based on the sequence data, the DHU-Pred model was proposed in this study to find possible D sites.

Methodology:

The model was built by employing comprehensive machine learning and feature extraction approaches. It was then validated using in-demand evaluation metrics and rigorous experimentation and testing approaches.

Results:

The DHU-Pred revealed an accuracy score of 96.9%, which was considerably higher compared to the existing D site predictors.

Availability And Implementation:

A user-friendly web server for the proposed model was also developed and is freely available for the researchers.

Keywords:

Classification DHU-Pred Dihydrouridine Machine learning Post Transcriptional Modification Prediction RNA Random Forest Statistical moments Uridine modifications

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

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

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...

Predicting Molecular Geometry

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries

Regioselectivity and Stereochemistry of Acid-Catalyzed Hydration

Regioselectivity and Stereochemistry of Acid-Catalyzed Hydration

The rate of acid-catalyzed hydration of alkenes depends on the alkene's structure, as the presence of alkyl substituents at the double bond can significantly influence the rate.

Predicting Reaction Outcomes

Predicting Reaction Outcomes

Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...

Classification of Titrimetric Analysis Based on Reaction Types

Classification of Titrimetric Analysis Based on Reaction Types

Titrimetric analysis in solution chemistry involves measuring the volume of solutions and is often called volumetric analysis. The standard solution of known concentration in the burette is called the titrant, whereas the solution of unknown concentration in the flask is called the analyte, or titrand. Titrimetric analyses can be classified into four types based on the reactions between the titrant and analyte.
Titrations between an acid and a base lead to neutralization reactions that form...

Predicting Products: Substitution vs. Elimination

Predicting Products: Substitution vs. Elimination

When a nucleophile and an alkyl halide react, nucleophilic substitution and β-elimination reactions compete to generate products.
The following factors can influence the mechanisms competing against each other:

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

Federated TinyML and digital twin framework for secure and resilient IoMT-based ICU monitoring.

Scientific reports·2026

A lightweight hybrid framework for real-time data refinement in resource-constrained underwater and underground wireless sensor networks.

Scientific reports·2026

predALZ: An Ensemble Learning Framework for Identifying Genetic Biomarkers in Familial Alzheimer's Disease.

Current drug targets·2026

HybridTrust: on-device federated learning with crypto-agile security for legacy and quantum-safe medical devices.

Scientific reports·2026

GlomNet: glomeruli segmentation network for WSI with diverse staining protocols for kidney disease diagnosis.

Frontiers in medicine·2026

A generative explainable model for antimicrobial peptide prediction using bidirectional temporal convolutional neural network.

Scientific reports·2026

See all related articles