Navigating the landscape of enzyme design: from molecular simulations to machine learning
J Zhou, M Huang - Chemical Society Reviews, 2024 - pubs.rsc.org
Global environmental issues and sustainable development call for new technologies for fine
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …
[HTML][HTML] Quantum mechanical-based strategies in drug discovery: Finding the pace to new challenges in drug design
The expansion of the chemical space to tangible libraries containing billions of
synthesizable molecules opens exciting opportunities for drug discovery, but also …
synthesizable molecules opens exciting opportunities for drug discovery, but also …
QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning …
Understanding the interaction of ligands with biomolecules is an integral component of drug
discovery and development. Challenges for computing thermodynamic and kinetic …
discovery and development. Challenges for computing thermodynamic and kinetic …
[HTML][HTML] How exascale computing can shape drug design: A perspective from multiscale QM/MM molecular dynamics simulations and machine learning-aided …
G Rossetti, D Mandelli - Current Opinion in Structural Biology, 2024 - Elsevier
Molecular simulations are an essential asset in the first steps of drug design campaigns.
However, the requirement of high-throughput limits applications mainly to qualitative …
However, the requirement of high-throughput limits applications mainly to qualitative …
All-Atom Biomolecular Simulation in the Exascale Era
Exascale supercomputers have opened the door to dynamic simulations, facilitated by AI/ML
techniques, that model biomolecular motions over unprecedented length and time scales …
techniques, that model biomolecular motions over unprecedented length and time scales …
PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics
JP Pederson, JG McDaniel - The Journal of Chemical Physics, 2024 - pubs.aip.org
PyDFT-QMMM is a Python-based package for performing hybrid quantum
mechanics/molecular mechanics (QM/MM) simulations at the density functional level of …
mechanics/molecular mechanics (QM/MM) simulations at the density functional level of …
Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness
Computational techniques applied to drug discovery have gained considerable popularity
for their ability to filter potentially active drugs from inactive ones, reducing the time scale …
for their ability to filter potentially active drugs from inactive ones, reducing the time scale …
QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis
Natural products and their derivatives are widely used across various industries, particularly
pharmaceuticals. Modern engineered biosynthesis provides an alternative way of producing …
pharmaceuticals. Modern engineered biosynthesis provides an alternative way of producing …
[HTML][HTML] Multiscale biomolecular simulations in the exascale era
The complexity of biological systems and processes, spanning molecular to macroscopic
scales, necessitates the use of multiscale simulations to get a comprehensive …
scales, necessitates the use of multiscale simulations to get a comprehensive …
[HTML][HTML] Biomolecular simulations at the exascale: From drug design to organelles and beyond
The rapid advancement in computational power available for research offers to bring not
only quantitative improvements, but also qualitative changes in the field of biomolecular …
only quantitative improvements, but also qualitative changes in the field of biomolecular …