Residue Level Three-dimensional Workspace Maps for Conformational Trajectory Planning of Proteins

摘要: The function of a protein macromolecule often requires conformational transitions between two native conformations. Understanding these is essential to the understanding how proteins function, as well ability design and manipulate protein-based nanomechanical systems. In this paper we propose set 3D Cartesian workspace maps for exploring pathways. These are constructed in Euclidean space triads chain segments molecules that have been shown high probability occurrence naturally observed based on data obtained from more than 38,600 Protein Data Bank (PDB). We show proposed propensity effective navigation tools angle space. argue main reason improved efficiency fact that, although there one-to-one mapping 2D dihedral maps, distributions significantly different spaces. Hence, allow pathway planning be performed directly propensities computed same space, which where change their