Sanal ortamlarda haptik geri beslemeli katı moleküler kenetlenme

In this thesis, we present computationally efficient methods for visualization andsimulation of molecular interactions in virtual environments with haptic feedback. In oursimulations, the haptic device is used to guide a rigid ligand molecule into a receptor sitewhile the molecular forces acting on the ligand molecule are scaled and reflected to the userin real-time. We demonstrate that the presence of a haptic interface accelerates the bindingprocess and reduce the binding errors if it is used as a precursor to estimate the initialconfiguration of the ligand molecule at the binding site. After placement and rough alignmentof the ligand molecule inside the binding cavity with the help of a haptic device, we use anovel computational approach to determine the final binding configuration of the ligandmolecule. In this approach, the ligand molecule is treated as a rigid body seeking for thelowest potential energy configuration. The rigid body configurations of the ligand moleculeis calculated in a least square sense using the new positions of its atoms moving under theinfluence of molecular interaction forces. The proposed approach is computationally moreefficient than the molecular simulation methods that utilize the standard rigid-bodyformulations. We also present new methods for haptic visualization of a protein surfaceinteractively to search for potential binding sites. Our experimental studies with 6 subjectsshow that subjects can successfully identify the true binding site among the 5 potentialbinding sites using visual and haptic cues. In addition, we show that the proposed distanceminimization approach can be used to find the final configuration of a ligand molecule insidethe binding cavity after it is initially aligned by the subject.