ProteinsPlus: a web portal for structure analysis of macromolecules

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• The Protein Data Bank (PDB) is a vast resource for structural biology research, with over 126,000 structures.
• Structure-driven research in drug discovery, crop science, and biotechnology relies heavily on computational tools for molecular analysis.

Purpose of the Study:

• To present ProteinsPlus, a unified web server offering a suite of tools for early-stage structure-based molecular modeling.
• To provide an easy-to-use interface for essential pre-processing and analysis tasks in structural bioinformatics.

Main Methods:

• Integration of multiple computational tools including EDIA for quality assessment, Protoss for hydrogen placement, and SIENA for conformational searches.
• Inclusion of tools for 2D interaction diagrams (PoseView), protein-protein interface classification (HyPPI), and pocket detection/druggability assessment (DoGSiteScorer).
• Development of a unified interface with intuitive visualization, parameterization, and download options.

Main Results:

• ProteinsPlus offers a comprehensive platform for structure-based molecular modeling.
• The server streamlines common workflows, from quality assessment to pocket analysis.
• Features include temporary storage of results for convenient access and communication.

Conclusions:

• ProteinsPlus provides a valuable, user-friendly resource for researchers in structural biology and related fields.
• The unified interface simplifies complex modeling tasks, accelerating research in drug discovery and biotechnology.
• The server facilitates efficient data handling and collaboration among researchers.