PlaneFinder: a methodology to find the best plane for a set of atoms involved in the metal coordination in protein structures

Abstract

Metal ions play a considerable role in protein structure and function. The roles of most metals and their importance are determined by the arrangements of the interacting atoms in the three-dimensional protein structure. This information is essential in predicting the geometry of the atoms involved in metal coordination. The deviation of the other atoms from the best plane is another crucial factor. The proposed web server, PlaneFinder, provides a fast and efficient method to calculate the best-fit plane for a set of atoms involved in the metal coordination. It provides in addition other possible planes by considering the maximum number of interacting atoms as well as user-selected atoms. The deviations of the selected atoms and other atoms from the best-fit plane are also displayed. PlaneFinder is freely available and can be accessed at http://bioserver1.physics. iisc.ac.in/plane/.