Macromolecular Modeling Blog ™

The Outcome of a workshop on applications of protein models in biomedical research. review summarizes a recent meeting (meeting website) held at UCSF. The case studies in this review may serve as an excellent resource for researchers that need to demonstrate the applicability and utility of macromolecular modeling for advancing experimental studies. In the author list from the Rosetta Commons were Tanja Kortemme and Rhiju Das. The author list is also a great resource for those that are new to the field and would like to familiarize themselves with some of the major figures.

An edited outline with links below is provided as an overview, reference, and primer for discussion topics:

• New Context for Modeling Provided by the Protein Structure Initiative
• Protein Structure Initiative Knowledgebase and Protein Model Portal
• Applications of Modeling for Biology and Medicine
  • Drug Discovery
  • Biotherapeutics, Biologicals, and Industrial Enzymes
  • Protein-Protein Interactions
  • Membrane Binding Specificity
  • Ligand Specificity of Receptors
  • Substrate Specificity of Enzymes
  • Analysis of Mutations
  • Cancer Biology
• Integrative or Hybrid Structure Determination Methods
  • Atomic Structure Determination
  • Structural Characterization of Large Assemblies at Low Resolution
• Recommendations
  • Standards for the Publication of Models Must Be Established
    • Journal Requirements
    • Model Access and Archiving
  • Standards for Data Formats Must Be Established to Facilitate Data and Software Exchange
  • Standards for the Assessment of Models Must Be Established
    • Model Accuracy Criteria
    • Estimating Model Accuracy
  • The Scientific Community Needs to Be Aware of the Strengths and Limitations of Models
  • The Protein Model Portal Can Play a Key Role

Torsten Schwede, Andrej Sali, Barry Honig, Michael Levitt, Helen M. Berman, David Jones, Steven E. Brenner, Stephen K. Burley, Rhiju Das, Nikolay V. Dokholyan (2009). Outcome of a Workshop on Applications of Protein Models in Biomedical Research Structure, 17 (2), 151-159 DOI: 10.1016/j.str.2008.12.014