Regine Bohacek
Boston De Novo Design
USA
Title: “Growing†Hydrogen Bonding Waters in Molecular Complexes
Biography
Biography: Regine Bohacek
Abstract
The goal of this work is to use fast algorithms from the denovo design program, AlleGrow (1), to accurately position explicit waters in a protein structure. The best source of precise data on water interactions in organic complexes is found in small molecule X-ray structures. The studies were done using packed X-ray structures which contain water taken from the Crystallographic Open Data
Base (COD, 2).
To test the growth algorithm, waters were removed one at a time and “regrown”. This search algorithm was optimized to ensure that the output contained water close to the experimental X-ray water. A scoring function was developed to rank order the water positions found in the search with the aim of identifying the water closest to the X-ray structure. The scoring function was optimized to obtain the best possible predictions for a large set of different experimental waters.