Binding free energy estimation of drug candidates to their biomolecular target is one of the best quantitative estimators in computer-aided drug discovery. Accurate binding free energy estimation is still a challengeable task even after decades of re...
Machine learning has been recently used to predict therapeutic antibody aggregation rates and viscosity at high concentrations (150 mg/ml). These works focused on commercially available antibodies, which may have been optimized for stability. In this...
Recent advances in deep learning frameworks have established valuable tools for analyzing the long-timescale behavior of complex systems, such as proteins. In particular, the inclusion of physical constraints, e.g., time-reversibility, was a crucial ...
Full-quantum mechanics (QM) calculations are extraordinarily precise but difficult to apply to large systems, such as biomolecules. Motivated by the massive demand for efficient calculations for large systems at the full-QM level and by the significa...
Proceedings of the National Academy of Sciences of the United States of America
Oct 19, 2021
The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 ha...
Biomacromolecules manifest dynamic conformational fluctuation and involve mutual interconversion among metastable states. A robust mapping of their conformational landscape often requires the low-dimensional projection of the conformational ensemble ...
Understanding the permeation of biomolecules through cellular membranes is critical for many biotechnological applications, including targeted drug delivery, pathogen detection, and the development of new antibiotics. To this end, computer simulation...
Proceedings of the National Academy of Sciences of the United States of America
Mar 9, 2021
Kinases play important roles in diverse cellular processes, including signaling, differentiation, proliferation, and metabolism. They are frequently mutated in cancer and are the targets of a large number of specific inhibitors. Surveys of cancer gen...
Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology
Mar 3, 2021
Although ion channels are crucial in many physiological processes and constitute an important class of drug targets, much is still unclear about their function and possible malfunctions that lead to diseases. In recent years, computational methods ha...
High viscosity presents a challenge for manufacturing and drug delivery of therapeutic antibodies. The viscosity is determined by protein-protein interactions among many antibodies. Molecular simulation is a promising method to study protein-protein ...
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