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The quality analysis workflow for predicted complexes

Nadzirin, Nurul

Most gene products, whether protein or RNA, perform their functions in cells by interacting with other gene products, forming complexes. The dysregulation or disruption of these complexes often leads to disease as they play a crucial role in all cellular processes. Characterizing protein-protein interactions and assemblies, and understanding the principles that governs them, are therefore more than ever at the center stage of today's molecular biology.

There is a good case for testing in silico methods that generate structural models of the assemblies by docking their components. The nature of docking experiments allows us to test our current understanding of the principles of macromolecular interactions, and also to encode our understanding in computational methods. All computational predictions hence need to be validated both in terms of model quality and also experimentally, to see how close the model is to an experimentally determined model. As docking methods improve, reliable models will greatly help in designing future experiments and to push the boundaries of currently available algorithms.

Since 2000, a community-wide effort called CAPRI (Critical Assessment of PRedicted Interactions) has been organized to do a large-scale, blind predictions of structures of complexes. CAPRI has allowed dozens of groups in the structural biology community to predict 130 complexes, offered by crystallographers as targets prior to publication. For this project, the aim is to expose the assessment method for public use, by providing a complex assessment server that users can upload their predicted complexes to and have the assessment geometry and quality results as output.

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