VAMPnets for deep learning of molecular kinetics
Sign Up to like & getrecommendations! Published in 2017 at "Nature Communications"
DOI: 10.1038/s41467-017-02388-1
Abstract: 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 transformation of simulated coordinates into structural… read more here.
Keywords: state; markov; learning molecular; molecular kinetics ... See more keywords
Machine learning molecular dynamics for the simulation of infrared spectra††Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc02267k
Sign Up to like & getrecommendations! Published in 2017 at "Chemical Science"
DOI: 10.1039/c7sc02267k
Abstract: Artificial neural networks are combined with molecular dynamics to simulate molecular infrared spectra including anharmonicities and temperature effects. read more here.
Keywords: machine learning; molecular dynamics; learning molecular; infrared spectra ... See more keywords
Learning the molecular grammar of protein condensates from sequence determinants and embeddings
Sign Up to like & getrecommendations! Published in 2021 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2019053118
Abstract: Significance The tendency of many cellular proteins to form protein-rich biomolecular condensates underlies the formation of subcellular compartments and has been linked to various physiological functions. Understanding the molecular basis of this fundamental process and… read more here.
Keywords: protein; phase separation; phase; learning molecular ... See more keywords
Machine learning and molecular design of self-assembling -conjugated oligopeptides
Sign Up to like & getrecommendations! Published in 2018 at "Molecular Simulation"
DOI: 10.1080/08927022.2018.1469754
Abstract: Abstract Self-assembling oligopeptides present a means to fabricate biocompatible supramolecular aggregates with engineered electronic and optical functionality. We conducted molecular dynamics simulations of self-assembling synthetic oligopeptides with Asp-X -X -X - -X -X -X -Asp… read more here.
Keywords: molecular design; machine learning; self assembling; learning molecular ... See more keywords
A Heterogeneous Parallel Non-von Neumann Architecture System for Accurate and Efficient Machine Learning Molecular Dynamics
Sign Up to like & getrecommendations! Published in 2023 at "IEEE Transactions on Circuits and Systems I: Regular Papers"
DOI: 10.1109/tcsi.2023.3255199
Abstract: This paper proposes a special-purpose system to achieve high-accuracy and high-efficiency machine learning (ML) molecular dynamics (MD) calculations. The system consists of field programmable gate array (FPGA) and application specific integrated circuit (ASIC) working in… read more here.
Keywords: system; machine learning; tex math; inline formula ... See more keywords
Machine learning for molecular simulation
Sign Up to like & getrecommendations! Published in 2020 at "Annual review of physical chemistry"
DOI: 10.1146/annurev-physchem-042018-052331
Abstract: Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for an ML revolution and have already been profoundly affected by the application of existing… read more here.
Keywords: machine learning; learning molecular; chemistry; molecular simulation ... See more keywords
Machine Learning for Molecular Modelling in Drug Design
Sign Up to like & getrecommendations! Published in 2019 at "Biomolecules"
DOI: 10.3390/biom9060216
Abstract: Machine learning (ML) has become a crucial component of early drug discovery. This researcharea has been fueled by two main factors [...]. read more here.
Keywords: machine; machine learning; learning molecular; modelling drug ... See more keywords
Evaluation of Docking Machine Learning and Molecular Dynamics Methodologies for DNA-Ligand Systems
Sign Up to like & getrecommendations! Published in 2022 at "Pharmaceuticals"
DOI: 10.3390/ph15020132
Abstract: DNA is a molecular target for the treatment of several diseases, including cancer, but there are few docking methodologies exploring the interactions between nucleic acids with DNA intercalating agents. Different docking methodologies, such as AutoDock… read more here.
Keywords: dna; docking machine; machine learning; evaluation docking ... See more keywords
Deep learning for molecular generation.
Sign Up to like & getrecommendations! Published in 2019 at "Future medicinal chemistry"
DOI: 10.4155/fmc-2018-0358
Abstract: De novo drug design aims to generate novel chemical compounds with desirable chemical and pharmacological properties from scratch using computer-based methods. Recently, deep generative neural networks have become a very active research frontier in de… read more here.
Keywords: learning molecular; deep learning; novo drug; generation ... See more keywords