Improving molecular docking through eHiTS’ tunable scoring function

We present three complementary approaches for score-tuning that improve docking performance in pose prediction, virtual screening and binding affinity assessment. The methodology utilizes experimental data to customize the scoring function for the system of interest considering the specific docking scenario. The tuning approach, which has been implemented as an automated utility in eHiTS, is introduced as a solution to one of the conundrums of the molecular docking paradigm, namely, the lack of a universally well performing scoring function. The accuracy of scoring functions has been shown to be generally system-dependent, and particularly lacking for binding energy and bio-activity predictions. In the proposed approach, pose and energy predictions are enhanced by adjusting the relative weights of the eHiTS energy terms to improve score-RMSD or score-affinity correlations. In a virtual screening context ligand-based similarity is used to rescale the docking score such that better enrichment factors are achieved. We discuss the algorithmic details of the methods, and demonstrate the effects of score tuning on a variety of targets, including CDK2, BACE1 and neuraminidase, as well as on the popular benchmarks—the Directory of Useful Decoys and the PDBBind database.     

Collision-induced rovibrational energy transfer in small polyatomic molecules: the role of intramolecular perturbations

ABSTRACT

Various forms of time-resolved optical double-resonance spectroscopy facilitate rotationally resolved measurements of collision-induced intramolecular vibration-to-vibration (V–V) energy-transfer processes, which take a gas-phase polyatomic molecule from one distinct rovibrational energy level to another. Of longstanding mechanistic interest are questions concerning the extent to which such V–V energy transfer (ET) may be influenced by intramolecular perturbations – notably Fermi resonance (and other anharmonic mixing effects) and Coriolis coupling – within polyatomic molecular rovibrational manifolds of interest. It is evident that quantum-mechanical interference effects can arise, either inhibiting or enhancing the probability of collision-induced ET in perturbed rovibrational manifolds of certain small gas-phase polyatomic molecules, notably CO₂, D₂CO and C₂H₂. This article focuses on a blend of high-resolution rovibrational spectroscopy (characterising initial and final molecular levels and their intramolecular perturbations) and collision dynamics (with colliding molecules defined in terms of isolated-molecule spectroscopic basis states). It aims to offer fresh insights and to consider some apparent mechanistic anomalies (e.g. collision-induced quasi-continuous background effects in the 4ν_CH rovibrational manifold of C₂H₂). Various reported experiments and related theoretical treatments are critically re-examined, in order to pose and address mechanistic questions some of which still challenge detailed understanding.