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ecs 129 Forewords Introduction Nucleic Acids Proteins: Amino Acids Proteins: Secondary and Tertiary Structures Sequence Comparison Protein Structure Classification RNA Structure Prediction Protein Structure Prediction Protein Protein Interaction Docking Lecture Notes Summary Supporting Papers Databases Review Quick links pakoehl@ucdavis.edu

Patrice Koehl's teaching web site > ecs 129 > Docking > Summary Personal tools Log in Summary Docking: Summary Docking is the computational procedure that predicts the conformation of a complex between 2 or more molecules Binding is central to many processes. It can be cooperative when several ligands are involved; in some cases, one ligand binds and induces a conformational change that allow a second ligand to bind (allostery) The classic view of docking involve rigid body transformation: this is the lock-and key view of docking It is known in fact that docking involves conformation changes, described as "induced fit" Even rigid-body docking is a computationally costly procedure as it involves 6 degrees of freedom (3 translations and 3 rotations). FFT-based methods for docking can save a significant amount of time. Probably the most popular docking program is DOCK, originally developed by Kuntz.

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