MolAxis: Efficient and accurate identification of channels in macromolecules

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Abstract
Channels and cavities play important roles in macromolecular functions, serving as access/exit routes for substrates/products, cofactor and drug binding, catalytic sites, and ligand/protein. In addition, channels formed by transmembrane (TM) proteins serve as transporters and ion channels. MolAxis is a new sensitive and fast tool for the identification and classification of channels and cavities of various sizes and shapes in macromolecules. MolAxis constructs corridors, which are pathways that represent probable routes taken by small molecules passing through channels. The outer medial axis of the molecule is the collection of points that have more than one closest atom. It is composed of two‐dimensional surface patches and can be seen as a skeleton of the complement of the molecule. We have implemented in MolAxis a novel algorithm that uses state‐of‐the‐art computational geometry techniques to approximate and scan a useful subset of the outer medial axis, thereby reducing the dimension of the problem and consequently rendering the algorithm extremely efficient. MolAxis is designed to identify channels that connect buried cavities to the outside of macromolecules and to identify TM channels in proteins. We apply MolAxis to enzyme cavities and TM proteins. We further utilize MolAxis to monitor channel dimensions along Molecular Dynamics trajectories of a human Cytochrome P450. MolAxis constructs high quality corridors for snapshots at picosecond time‐scale intervals substantiating the gating mechanism in the 2e substrate access channel. We compare our results with previous tools in terms of accuracy, performance and underlying theoretical guarantees of finding the desired pathways. MolAxis is available on line as a web‐server and as a standalone easy‐to‐use program (http://bioinfo3d.cs.tau.ac.il/MolAxis/). Proteins 2008.