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Updated: Sep 22, 2025
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
68.9K
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures
David Jakubec1, Petr Skoda1, Radoslav Krivak1
1Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Czech Republic.
Nucleic Acids Research
|May 24, 2022
Summary
PrankWeb now offers enhanced protein-ligand binding site (LBS) predictions using improved evolutionary conservation and AlphaFold models. This update facilitates drug design and protein function studies.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Protein-ligand binding sites (LBSs) are crucial for understanding protein function and enabling structure-based drug design.
- Previous work established P2Rank and PrankWeb for efficient LBS prediction.
Purpose of the Study:
- To present significant enhancements to the PrankWeb server for improved LBS prediction.
- To expand the utility of PrankWeb for researchers lacking experimental protein structures.
Main Methods:
- Implemented a new evolutionary conservation estimation pipeline using UniRef50 and HMMER3.
- Integrated AlphaFold model database access for predictions without experimental structures.
- Introduced Docker container deployment, mmCIF format support, and enhanced REST API.
Main Results:
- Achieved more accurate LBS predictions through an improved evolutionary conservation pipeline.
- Enabled LBS prediction for proteins lacking experimental structures via AlphaFold integration.
- Enhanced usability with Docker, mmCIF support, improved API, and batch download capabilities.
Conclusions:
- The enhanced PrankWeb server provides more accurate and versatile LBS predictions.
- These improvements support a wider range of research, from basic science to drug discovery.
- The updated tool facilitates broader accessibility and application in structural bioinformatics.
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