Abstract
The ATTRACT protein-protein docking program has been employed to predict protein-protein complex structures in CAPRI rounds 38-45. For 11 out of 16 targets acceptable or better quality solutions have been submitted (~70%). It includes also several cases of peptide-protein docking and the successful prediction of the geometry of carbohydrate-protein interactions. The option of combining rigid body minimization and simultaneous optimization in collective degrees of freedom based on elastic network modes was employed and systematically evaluated. Application to a large benchmark set indicates a modest improvement in docking performance compared to rigid docking. Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed.
Highlights
The interaction of proteins to form functional complexes is a fundamental property of all living systems
In the field of protein-protein docking, the methodology has been further developed in several studies[13,14,42] and implemented in docking approaches such as ATTRACT14 and SwarmDock.[42]
With our recent GPU-based implementation protein-protein docking based on energy minimization starting from tens of thousands of start configurations can be performed within a few minutes of computer time for a medium sized complex including energy minimization in normal modes
Summary
The interaction of proteins to form functional complexes is a fundamental property of all living systems. It is possible to find a homologous complex in the database of known complexes to generate a template-based model.[1] in particular for transient protein-protein interactions or low-affinity complexes it is still difficult to determine the complex structure experimentally or based on a homologous template. The ATTRACT CG protein model represents each amino acid of a protein by up to four pseudo centers and is intermediate between a residue-level and full atomistic description.[11,12] In contrast to most protein-protein docking methods, the ATTRACT approach includes conformational flexibility of binding partners already approximately during the early systematic stage of protein-protein docking. Refinement efforts at atomic resolution to improve CAPRI protein-protein docking target predictions will be reported
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