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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.
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

BindUP-Alpha: A Webserver for Predicting DNA-and RNA-binding Proteins based on Experimental and Computational

Dina Alexandrovich¹, Shani Kagan², Yael Mandel-Gutfreund³

¹Technion-Israel Institute of Technology, Faculty of Biology, Emerson Building, Haifa, Israel.

Journal of Molecular Biology

|May 31, 2025

Summary

This summary is machine-generated.

BindUP-Alpha predicts nucleic acid binding proteins using protein structure and surface electrostatics. This tool aids in characterizing protein function from both experimental and predicted structures.

Keywords:

DNA-binding proteins RNA-binding proteins function prediction machine learning

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Published on: January 26, 2024

Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Protein structure is crucial for function.
AI tools like AlphaFold generate many protein models.
Disordered regions in models challenge function prediction.

Purpose of the Study:

To present BindUP-Alpha, an upgraded webserver for predicting nucleic acid binding proteins.
To improve protein function characterization using predicted structures.

Main Methods:

Structure-based algorithm using electrostatic and physiochemical properties.
Support Vector Machine (SVM) learning approach.
Utilizes experimentally solved and predicted protein structures.

Main Results:

BindUP-Alpha accurately predicts DNA- and RNA-binding proteins.
Identifies potential nucleic acid binding interfaces on protein surfaces.
Successfully analyzes both experimental and AI-predicted protein models.

Conclusions:

BindUP-Alpha enhances the prediction of nucleic acid binding proteins.
Provides valuable insights into protein function from structural data.
Offers interactive visualizations and downloadable results via a webserver.