title: A New Tabu-Search-Based Algorithm for Solvation of Proteins.
abstract: The proper description of explicit water shells is of enormous importance for all-atom calculations. We propose a new approach for the setup of water shells around proteins based on Tabu-Search global optimization and compare its efficiency with standard molecular dynamics protocols using the chignolin protein as a test case. Both algorithms generate reasonable water shells, but the new approach provides solvated systems with an increased water-enzyme interaction and offers further advantages. It enables a stepwise buildup of the solvent shell, so that the more important inner part can be prepared more carefully. It also allows the generation of solute structures which can be biased either toward the (experimental) starting structure or the underlying theoretical model, i.e., the employed force field.
authors.affiliation: Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Grebner
authors.affiliation: Universität Stuttgart, Institut für Theoretische Chemie, Pfaffenwaldring 55, D-70569 Stuttgart, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Kästner
authors.affiliation: Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany.
authors.forename: Walter
authors.initials: W
authors.lastname: Thiel
authors.affiliation: Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Engels