SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

Area of Science:

• Computational biology
• Structural biology
• Bioinformatics

Background:

• Protein structure homology modeling is crucial for understanding protein function when experimental data is lacking.
• Automated servers simplify the generation of 3D protein models, eliminating the need for specialized software or large databases.

Purpose of the Study:

• To describe the latest version of the SWISS-MODEL expert system for protein structure modeling.
• To highlight enhancements in template selection, model quality estimation, and user interface.

Main Methods:

• Utilized an improved SWISS-MODEL pipeline with extensive model quality estimation for template selection.
• Integrated quaternary structure and ligand annotations into the template library.
• Developed a new web interface for interactive template searching, clustering, and structural comparison.

Main Results:

• The enhanced SWISS-MODEL system provides estimates of resulting model accuracy.
• The system supports building complete structural models, including oligomeric states.
• User-guided template selection enables modeling of proteins in different functional states.

Conclusions:

• The latest SWISS-MODEL version offers a robust and user-friendly platform for generating reliable protein 3D models.
• Continuous evaluation by the CAMEO system ensures ongoing accuracy assessment.
• SWISS-MODEL facilitates structural modeling for a wide range of research applications.