No abstract

The formation of a covalent bond with the target is essential for a number of successful drugs, yet tools for covalent docking without significant restrictions regarding warhead or receptor classes are rare and limited in use. In this work we present DOCKTITE, a highly versatile workflow for covalent docking in the Molecular Operating Environment (MOE) combining automated warhead screening, nucleophilic side chain attachment, pharmacophore-based docking, and a novel consensus scoring approach. The comprehensive validation study includes pose predictions of 35 protein/ligand complexes which resulted in a mean RMSD of 1.74 Å and a prediction rate of 71.4% with an RMSD below 2 Å, a virtual screening with an area under the curve (AUC) for the receiver operating characteristics (ROC) of 0.81, and a significant correlation between predicted and experimental binding affinities (ρ = 0.806, R(2) = 0.649, p < 0.005).

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels control spontaneous electrical activity in heart and brain. Binding of cAMP to the cyclic nucleotide-binding domain (CNBD) facilitates channel opening by relieving a tonic inhibition exerted by the CNBD. Despite high resolution structures of the HCN1 channel in the cAMP bound and unbound states, the structural mechanism coupling ligand binding to channel gating is unknown. Here we show that the recently identified helical HCN-domain (HCND) mechanically couples the CNBD and channel voltage sensing domain (VSD), possibly acting as a sliding crank that converts the planar rotational movement of the CNBD into a rotational upward displacement of the VSD. This mode of operation and its impact on channel gating are confirmed by computational and experimental data showing that disruption of critical contacts between the three domains affects cAMP- and voltage-dependent gating in three HCN isoforms.

The Bitcoin network of decentralized payment transactions has attracted a lot of attention from both Internet users and researchers in recent years. Bitcoin utilizes a peer-to-peer network to issue anonymous payment transactions between different users. In the currently used Bitcoin clients, the full transaction history is available at each node of the network to prevent double spending without the need for a central authority, forming a valuable source for empirical research on network structure, network dynamics, and the implied anonymity challenges, as well as guidance on the future evolution of complex payment systems. We found dynamical effects of which some increase anonymity while others decrease it. Most importantly, several parameters of the Bitcoin transaction graph seem to have become stationary over the last 12–18 months. We discuss the implications

We investigate a novel stochastic technique for the global optimization of complex potential energy surfaces (PES) that avoids the freezing problem of simulated annealing by allowing the dynamical process to tunnel energetically inaccessible regions of the PES by way of a dynamically adjusted nonlinear transformation of the original PES. We demonstrate the success of this approach, which is characterized by a single adjustable parameter, for three generic hard minimization problems.