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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
Published on: July 8, 2025
In silico protein motif discovery and structural analysis
Catherine Mooney1, Norman Davey, Alberto J M Martin
1Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland. catherine.mooney@ucd.ie
Methods in Molecular Biology (Clifton, N.J.)
|July 23, 2011
Summary
This chapter reviews common in silico tools for protein motif discovery and structural analysis, guiding biologists in their application. It details Distill web servers for predicting protein structural features and 3D models from sequences.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Numerous in silico tools exist for protein motif discovery and structural analysis.
- Biologists require guidance on selecting and utilizing these computational resources effectively.
Purpose of the Study:
- To compile and explain commonly used in silico tools for protein analysis.
- To provide a practical guide for biologists in applying these tools.
Main Methods:
- Detailed explanation of the Distill web server suite for predicting protein structural features and 3D models.
- Pointers to additional tools for motif discovery, secondary and tertiary structure prediction.
- Brief discussion on predicting protein intrinsic disorder, functional sites, and Short Linear Motifs (SLiMs).
Main Results:
- A curated collection of useful in silico tools for protein structure and motif analysis is presented.
- Guidance is provided on the application of these tools, including the Distill web server.
- Considerations for balancing speed, accuracy, and scale in tool selection are highlighted.
Conclusions:
- The chapter serves as a valuable resource for biologists seeking to leverage in silico tools for protein research.
- Effective use of these tools aids in understanding protein structure, function, and dynamics.
- Informed selection of computational methods is crucial for successful protein motif discovery and structural analysis.
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