A novel measure to analyze protein structures: Aspect ratio in protein alpha shapes.

Proteins' three-dimensional (3D) structures are analyzed traditionally using geometric descriptors such as torsional angles and inter-atomic distances. In this study a measure that is borrowed from computational geometry, aspect ratio of each tetrahedron in alpha shapes of proteins, is utilized. This geometric descriptor differentiates alpha and beta structural classes of proteins when combined with principal components analysis. The method converts the structures of individual proteins, 3D coordinates of the atoms, to points on a plane. It has a high degree of accuracy in differentiating R and T structures of hemoglobin. Therefore, it is anticipated that the geometric measure can be used successfully in a method that is extended to solve classification problems in machine learning.

Reaction dynamics through kinetic transition states.

The transformation of a system from one state to another is often mediated by a bottleneck in the system's phase space. In chemistry, these bottlenecks are known as transition states through which the system has to pass in order to evolve from reactants to products. The chemical reactions are usually associated with configurational changes where the reactants and products states correspond, e.g., to two different isomers or the undissociated and dissociated state of a molecule or cluster. In this Letter, we report on a new type of bottleneck which mediates kinetic rather than configurational changes. The phase space structures associated with such kinetic transition states and their dynamical implications are discussed for the rotational vibrational motion of a triatomic molecule. An outline of more general related phase space structures with important dynamical implications is given.