G protein-coupled receptors (GPCRs) play a key role in many cellular signaling mechanisms, and must select among multiple coupling possibilities in a ligand-specific manner in order to carry out a myriad of functions in diverse cellular contexts. Muc...
Large-scale atomistic computer simulations of materials heavily rely on interatomic potentials predicting the energy and Newtonian forces on atoms. Traditional interatomic potentials are based on physical intuition but contain few adjustable paramete...
Journal of chemical theory and computation
May 14, 2019
In recent years, machine learning (ML) methods have become increasingly popular in computational chemistry. After being trained on appropriate ab initio reference data, these methods allow for accurately predicting the properties of chemical systems,...
Flexibility is often a key determinant of protein function. To elucidate the link between their molecular structure and role in an organism, computational techniques such as molecular dynamics can be leveraged to characterize their conformational spa...
Journal of chemical information and modeling
Apr 2, 2019
It has demonstrated that glycogen synthase kinase 3β (GSK3β) is related to Alzheimer's disease (AD). On the basis of the world largest traditional Chinese medicine (TCM) database, a network-pharmacology-based approach was utilized to investigate TCM ...
Soft robots exhibit many exciting properties due to their softness and body compliance. However, to interact with the environment safely and to perform a task effectively, a soft robot faces a series of challenges such as dexterous motion, propriocep...
Current opinion in structural biology
Mar 23, 2019
While G-protein-coupled receptors (GPCRs) constitute the largest class of membrane proteins, structures and endogenous ligands of a large portion of GPCRs remain unknown. Because of the involvement of GPCRs in various signaling pathways and physiolog...
Proceedings of the National Academy of Sciences of the United States of America
Feb 26, 2019
The lysosomal enzyme glucocerebrosidase-1 (GCase) catalyzes the cleavage of a major glycolipid glucosylceramide into glucose and ceramide. The absence of fully functional GCase leads to the accumulation of its lipid substrates in lysosomes, causing G...
Journal of the American Chemical Society
Feb 21, 2019
Despite tremendous progress in understanding and engineering enzymes, knowledge of how enzyme structures and their dynamics induce observed catalytic properties is incomplete, and capabilities to engineer enzymes fall far short of industrial needs. H...
For exploration of chemical and biological systems, the combined quantum mechanics and molecular mechanics (QM/MM) and machine learning (ML) models have been developed recently to achieve high accuracy and efficiency for molecular dynamics (MD) simul...