Project Summary/Abstract
The mission of the Hamelberg group is to develop computational tools to complement
experiments in elucidating the dynamics-function relationship in biomolecules. The group has
been continuously making significant contributions to theoretical biochemistry and biophysics,
including developing methods for enhanced sampling, free energy calculation, and the analysis
of biomolecular dynamic data, and their applications to diverse biological systems. These
methods, based on molecular dynamics, can reveal at the atomic level of detail the mechanism
of biomolecular function, which is usually difficult to obtain by current experiments. Such detailed
knowledge is essential for the understanding and fine-tuning of (patho)physiological processes,
which can be leveraged for drug discovery and biomolecular design. The group is dedicated to
continuing this endeavor by developing innovative computational tools that are more intimately
coupled with experiments, implementing more advanced algorithms able to better identify
function-related information from complex data, accompanied by well-established systems for
rigorously checking convergence, robustness, and accuracy, and accessible to the broader
community of biochemists. These tools will be tested on diverse biological systems of
pharmaceutical significance. Our work will help resolve the current challenge that, with the rapid
growth of computing power, longer molecular simulations are routinely performed but efficient
computational tools to transform the data into knowledge are missing. We envisage that these
tools will largely enhance the effectiveness of using molecular simulations to interpret
experimental observations and guide new experimental designs by making testable predictions
or hypothesis, hence promoting more collaborations between computational and experimental
labs that will eventually accelerate new biological discoveries.
