Molecular dynamics simulations in drug discovery and pharmaceutical development

OMH Salo-Ahen, I Alanko, R Bhadane, AMJJ Bonvin… - Processes, 2020 - mdpi.com
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

Enhanced sampling with machine learning

S Mehdi, Z Smith, L Herron, Z Zou… - Annual Review of …, 2024 - annualreviews.org
Molecular dynamics (MD) enables the study of physical systems with excellent
spatiotemporal resolution but suffers from severe timescale limitations. To address this …

Crystal nucleation in liquids: Open questions and future challenges in molecular dynamics simulations

GC Sosso, J Chen, SJ Cox, M Fitzner… - Chemical …, 2016 - ACS Publications
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing
an important role in areas such as climate change and the production of drugs. As the early …

Driving and characterizing nucleation of urea and glycine polymorphs in water

Z Zou, ER Beyerle, ST Tsai… - Proceedings of the …, 2023 - National Acad Sciences
Crystal nucleation is relevant across the domains of fundamental and applied sciences.
However, in many cases, its mechanism remains unclear due to a lack of temporal or spatial …

Entropy based fingerprint for local crystalline order

PM Piaggi, M Parrinello - The Journal of chemical physics, 2017 - pubs.aip.org
We introduce a new fingerprint that allows distinguishing between liquid-like and solid-like
atomic environments. This fingerprint is based on an approximate expression for the entropy …

Molecular-dynamics simulations of urea nucleation from aqueous solution

M Salvalaglio, C Perego, F Giberti… - Proceedings of the …, 2015 - National Acad Sciences
Despite its ubiquitous character and relevance in many branches of science and
engineering, nucleation from solution remains elusive. In this framework, molecular …

Machine learning nucleation collective variables with graph neural networks

FM Dietrich, XR Advincula, G Gobbo… - Journal of Chemical …, 2023 - ACS Publications
The efficient calculation of nucleation collective variables (CVs) is one of the main limitations
to the application of enhanced sampling methods to the investigation of nucleation …

Review of liquid–liquid phase separation in crystallization: from fundamentals to application

S Xu, H Zhang, B Qiao, Y Wang - Crystal Growth & Design, 2021 - ACS Publications
In the field of industrial crystallization, liquid–liquid phase separation (LLPS) easily makes
the crystallization process into an uncontrollable state, making it extremely difficult for people …

Enhancing entropy and enthalpy fluctuations to drive crystallization in atomistic simulations

PM Piaggi, O Valsson, M Parrinello - Physical review letters, 2017 - APS
Crystallization is a process of great practical relevance in which rare but crucial fluctuations
lead to the formation of a solid phase starting from the liquid. As in all first order first …

Analyzing and driving cluster formation in atomistic simulations

GA Tribello, F Giberti, GC Sosso… - Journal of chemical …, 2017 - ACS Publications
In this paper a set of computational tools for identifying the phases contained in a system
composed of atoms or molecules is introduced. The method is rooted in graph theory and …