Single-molecule experiments and molecular dynamics (MD) simulations are indispensable tools for investigating protein conformational dynamics. The former provide data, such as donor-acceptor distances, whereas the latter give atomistic information, ...
Aqueous solubility and partition coefficient are important physical properties of small molecules. Accurate theoretical prediction of aqueous solubility and partition coefficient plays an important role in drug design and discovery. The prediction ac...
Allostery is a process by which proteins transmit the effect of perturbation at one site to a distal functional site upon certain perturbation. As an intrinsically global effect of protein dynamics, it is difficult to associate protein allostery with...
Journal of chemical information and modeling
Mar 7, 2018
Parametrization of small organic molecules for classical molecular dynamics simulations is not trivial. The vastness of the chemical space makes approaches using building blocks challenging. The most common approach is therefore an individual paramet...
Journal of biomolecular structure & dynamics
Mar 2, 2018
Thrombin is a key component for chemotherapeutic and antithrombotic therapy development. As the physiologic and pathologic roles of the light chain still remain vague, here, we continue previous efforts to understand the impacts of the disease-associ...
Current opinion in structural biology
Feb 21, 2018
Classical molecular dynamics (MD) simulations will be able to reach sampling in the second timescale within five years, producing petabytes of simulation data at current force field accuracy. Notwithstanding this, MD will still be in the regime of lo...
This work introduces a number of algebraic topology approaches, including multi-component persistent homology, multi-level persistent homology, and electrostatic persistence for the representation, characterization, and description of small molecules...
There is an increasing demand for computing the relevant structures, equilibria, and long-timescale kinetics of biomolecular processes, such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transfor...
Journal of materials science. Materials in medicine
Dec 30, 2017
In vitro, pancreatic β-cells tend to reduce their ability to aggregate into islets and lose insulin-producing ability, likely due to insufficient cell-cell and cell-matrix interactions that are essential for β-cell retention, viability and functional...
For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequ...