Protein-protein docking with F(2)Dock 2.0 and GB-rerank.

Motivation: Computational simulation of protein-protein docking can expedite the process of molecular modeling and drug discovery. This paper reports on our new F(2) Dock protocol which improves the state of the art in initial stage rigid body exhaustive docking search, scoring and ranking by introducing improvements in the shape-complementarity and electrostatics affinity functions, a new knowledge-based interface propensity term with FFT formulation, a set of novel knowledge-based filters and finally a solvation energy (GBSA) based reranking technique. Our algorithms are based on highly efficient data structures including the dynamic packing grids and octrees which significantly speed up the computations and also provide guaranteed bounds on approximation error.

1H[19F] NOE NMR structural signatures of the insulin R6 hexamer: evidence of a capped HisB10 site in aryl- and arylacryloyl-carboxylate complexes.

NEW AND IMPROVED INSULIN: 1H[19F] NOE NMR difference spectra for CF(3)-substituted aromatic carboxylates bound at the HisB10 sites of the R(6) human insulin (HI) hexamer show strong NOEs between the CF(3) groups and the LeuB6, AsnB3, and PheB1 sidechains. The NOEs and structural modeling establish that these carboxylates form closed complexes with the HisB10 site capped by the PheB1 rings.