Doing a good turn: the use of quaternions for rotation in molecular docking

A two-layer mono-objective algorithm based on guided optimization to reduce the computational cost in virtual screening

Virtual screening methods focus on searching molecules with similar properties to a given compound. Molecule databases are made up of large numbers of compounds and are constantly increasing. Therefore, fast and efficient methodologies and tools have to be designed to explore them quickly. In this context, ligand-based virtual screening methods are a well-known and helpful tool. These methods focus on searching for the most similar molecules in a database to a reference one. In this work, we propose a new tool called 2L-GO-Pharm, which requires less computational effort than OptiPharm, an efficient and robust piece of software recently proposed in the literature. The new-implemented tool maintains or improves the quality of the solutions found by OptiPharm, and achieves it by considerably reducing the number of evaluations needed. Some of the strengths that help 2L-GO-Pharm enhance searchability are the reduction of the search space dimension and the introduction of some circular limits for the angular variables. Furthermore, to ensure a trade-off between exploration and exploitation of the search space, it implements a two-layer strategy and a guided search procedure combined with a convergence test on the rotation axis. The performance of 2L-GO-Pharm has been tested by considering two different descriptors, i.e. shape similarity and electrostatic potential. The results show that it saves up to 87.5 million evaluations per query molecule.

Quantitative Characterization of Domain Motions in Molecular Machines

The work of molecular machines such as the ribosome is accompanied by conformational changes, often characterized by relative motions of their domains. The method we have developed seeks to quantify these motions in a general way, facilitating comparisons of results obtained by different researchers. Typically there are multiple snapshots of a structure in the form of pdb coordinates resulting from flexible fitting of low-resolution density maps, from X-ray crystallography, or from molecular dynamics simulation trajectories. Our objective is to characterize the motion of each domain as a coordinate transformation using moments of inertia tensor, a method we developed earlier. What has been missing until now are ancillary tools that make this task practical, general, and biologically informative. We have provided a comprehensive solution to this task with a set of tools implemented on the VMD platform. These tools address the need for reproducible segmentation of domains, and provide a generalized description of their motions using principal axes of inertia. Although this methodology has been specifically developed for studying ribosome motion, it is applicable to any molecular machine.