AlphaFold has burst into our lives. A powerful algorithm that underscores the strength of biological sequence data and artificial intelligence (AI). AlphaFold has appended projects and research directions. The database it has been creating promises a...
Molecular self-diffusion coefficients underlie various kinetic properties of the liquids involved in chemistry, physics, and pharmaceutics. In this study, 547 self-diffusion coefficients are calculated based on all-atom molecular dynamics (MD) simula...
Journal of chemical theory and computation
Aug 4, 2022
Machine-learning-based interatomic potential energy surface (PES) models are revolutionizing the field of molecular modeling. However, although much faster than electronic structure schemes, these models suffer from costly computations via deep neura...
Proceedings of the National Academy of Sciences of the United States of America
Aug 4, 2022
Using simulations or experiments performed at some set of temperatures to learn about the physics or chemistry at some other arbitrary temperature is a problem of immense practical and theoretical relevance. Here we develop a framework based on stati...
Identifying native-like protein-ligand complexes (PLCs) from an abundance of docking decoys is critical for large-scale virtual drug screening in early-stage drug discovery lead searching efforts. Providing reliable prediction is still a challenge fo...
Journal of physics. Condensed matter : an Institute of Physics journal
Jul 22, 2022
When creating training data for machine-learned interatomic potentials (MLIPs), it is common to create initial structures and evolve them using molecular dynamics (MD) to sample a larger configuration space. We benchmark two other modalities of evolv...
Journal of chemical theory and computation
Jul 15, 2022
Existing computational methods for estimating p values in proteins rely on theoretical approximations and lengthy computations. In this work, we use a data set of 6 million theoretically determined p shifts to train deep learning models, which are sh...
Journal of chemical information and modeling
Jul 5, 2022
The principle of least action is the cornerstone of classical mechanics, theory of relativity, quantum mechanics, and thermodynamics. Here, we describe how a neural network (NN) learns to find the trajectory for a Lennard-Jones (LJ) system that maint...
European journal of medicinal chemistry
Jul 1, 2022
Artificial intelligence (AI) has been recognized as a powerful technique that can accelerate drug discovery during the hit compound identification step. However, most simple deep learning models have been used for naive pre-filtering as the predictio...
NIMA-related kinase7 (NEK7) plays a multifunctional role in cell division and NLRP3 inflammasone activation. A typical expression or any mutation in the genetic makeup of NEK7 leads to the development of cancer malignancies and fatal inflammatory dis...