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Related Experiment Video

Updated: Oct 13, 2025

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

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DeepREx-WS: A web server for characterising protein-solvent interaction starting from sequence.

Matteo Manfredi¹, Castrense Savojardo¹, Pier Luigi Martelli¹

¹Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.

Computational and Structural Biotechnology Journal

|November 12, 2021

Summary

This study introduces DeepREx-WS, a web server integrating protein residue exposure, conservation, flexibility, and disorder. It aids in identifying key regions for protein surface engineering and stability modification.

Keywords:

Deep Learning Protein disorder Protein flexibility Residue solvent accessibility Surface engineering

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Published on: July 16, 2017

Area of Science:

Biochemistry
Computational Biology
Protein Engineering

Background:

Protein structure and function are influenced by residue exposure and flexibility.
Understanding protein-solvent interactions is crucial for surface engineering, especially when structural data is limited.

Purpose of the Study:

To develop a web server (DeepREx-WS) that integrates multiple features for analyzing protein residue properties.
To provide a tool for identifying critical regions in protein sequences for stability modification and surface engineering.

Main Methods:

Development of DeepREx, a deep learning tool for classifying residues as buried or exposed.
Integration of DeepREx predictions with residue conservation, hydrophobicity, flexibility, secondary structure, and disorder data.
Benchmarking DeepREx on a diverse dataset from the Protein Data Bank.

Main Results:

DeepREx achieves state-of-the-art performance in residue exposure prediction.
DeepREx-WS offers a comprehensive platform for analyzing protein sequence features.
The server facilitates the identification of residues for targeted protein modification.

Conclusions:

DeepREx-WS enhances the understanding of protein integrity by combining diverse sequence and structural features.
The web server is a valuable resource for protein surface engineering and biotechnological applications.
Integrating residue exposure with other properties aids in rational protein design.