Scientific discovery in the age of artificial intelligence
Artificial intelligence (AI) is being increasingly integrated into scientific discovery to augment
and accelerate research, helping scientists to generate hypotheses, design experiments …
and accelerate research, helping scientists to generate hypotheses, design experiments …
New Insights into the Cooperativity and Dynamics of Dimeric Enzymes
KW Chen, TY Sun, YD Wu - Chemical Reviews, 2023 - ACS Publications
A survey of protein databases indicates that the majority of enzymes exist in oligomeric
forms, with about half of those found in the UniProt database being homodimeric …
forms, with about half of those found in the UniProt database being homodimeric …
Direct generation of protein conformational ensembles via machine learning
Dynamics and conformational sampling are essential for linking protein structure to
biological function. While challenging to probe experimentally, computer simulations are …
biological function. While challenging to probe experimentally, computer simulations are …
Adaptive sampling methods for molecular dynamics in the era of machine learning
Molecular dynamics (MD) simulations are fundamental computational tools for the study of
proteins and their free energy landscapes. However, sampling protein conformational …
proteins and their free energy landscapes. However, sampling protein conformational …
Multiagent reinforcement learning-based adaptive sampling for conformational dynamics of proteins
DE Kleiman, D Shukla - Journal of Chemical Theory and …, 2022 - ACS Publications
Machine learning is increasingly applied to improve the efficiency and accuracy of molecular
dynamics (MD) simulations. Although the growth of distributed computer clusters has …
dynamics (MD) simulations. Although the growth of distributed computer clusters has …
Strategy to improve Cu-BTC metal-organic frameworks performance in removal of Rhodamine B: MD and WT-MtD simulations assessment
With industry progress, environmental problems have begun to threaten human health.
Among them, water pollution is closely related to human life and has attracted researchers' …
Among them, water pollution is closely related to human life and has attracted researchers' …
Active learning of the conformational ensemble of proteins using maximum entropy VAMPNets
DE Kleiman, D Shukla - Journal of Chemical Theory and …, 2023 - ACS Publications
Rapid computational exploration of the free energy landscape of biological molecules
remains an active area of research due to the difficulty of sampling rare state transitions in …
remains an active area of research due to the difficulty of sampling rare state transitions in …
Simulate time-integrated coarse-grained molecular dynamics with geometric machine learning
X Fu - 2022 - dspace.mit.edu
Molecular dynamics (MD) simulation is the workhorse of various scientific domains but is
limited by high computational cost. Learning-based force fields have made major progress …
limited by high computational cost. Learning-based force fields have made major progress …
An equivariant generative framework for molecular graph-structure co-design
Designing molecules with desirable physiochemical properties and functionalities is a long-
standing challenge in chemistry, material science, and drug discovery. Recently, machine …
standing challenge in chemistry, material science, and drug discovery. Recently, machine …
Simulation and machine learning methods for ion-channel structure determination, mechanistic studies and drug design
Ion channels are expressed in almost all living cells, controlling the in-and-out
communications, making them ideal drug targets, especially for central nervous system …
communications, making them ideal drug targets, especially for central nervous system …