A New Tabu-Search-Based Algorithm for Solvation of Proteins.

Area of Science:

• Computational chemistry
• Molecular modeling
• Biophysics

Background:

• Accurate explicit water shell description is crucial for all-atom molecular simulations.
• Standard molecular dynamics protocols have limitations in setting up these water shells.

Purpose of the Study:

• To introduce and evaluate a new Tabu-Search global optimization approach for setting up explicit water shells around proteins.
• To compare this novel method against standard molecular dynamics protocols.

Main Methods:

• Utilized Tabu-Search global optimization for water shell setup.
• Employed standard molecular dynamics protocols as a benchmark.
• Used the chignolin protein as a test case for both methods.

Main Results:

• Both Tabu-Search and standard methods produced reasonable water shells.
• The Tabu-Search approach resulted in increased water-enzyme interactions.
• The new method allows for stepwise solvent shell construction and bias control.

Conclusions:

• The proposed Tabu-Search method offers advantages for setting up explicit water shells in all-atom calculations.
• This approach enables more careful preparation of the inner solvent shell and flexible solute structure generation.
• The method enhances simulation accuracy by improving water-protein interactions.