Structural assembly of two-domain proteins by rigid-body docking

Background: Modelling proteins with multiple domains is one of the central challenges in Structural Biology. Although homology modelling has successfully been applied for prediction of protein structures, very often domain-domain interactions cannot be inferred from the structures of homologues and their prediction requires ab initio methods. Here we present a new structural prediction approach for modelling two-domain proteins based on rigid-body domain-domain docking. Results: Here we focus on interacting domain pairs that are part of the same peptide chain and thus have an inter-domain peptide region (so called linker). We have developed a method called pyDockTET (tethered-docking), which uses rigid-body docking to generate domain-domain poses that are further scored by binding energy and a pseudo-energy term based on restraints derived from linker end-to-end distances. The method has been benchmarked on a set of 77 non-redundant pairs of domains with available X-ray structure. We ...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Tammy M. K. Cheng, Tom L. Blundell, Juan Fernández-Recio
• Keywords: BMCBI 2008, Modelling, Prediction, Proteins