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 …

The effects of temperature on aerobic metabolism: towards a mechanistic understanding of the responses of ectotherms to a changing environment

PM Schulte - The Journal of experimental biology, 2015 - journals.biologists.com
Because of its profound effects on the rates of biological processes such as aerobic
metabolism, environmental temperature plays an important role in sha** the distribution …

HTMD: high-throughput molecular dynamics for molecular discovery

S Doerr, MJ Harvey, F Noé… - Journal of chemical …, 2016 - ACS Publications
Recent advances in molecular simulations have allowed scientists to investigate slower
biological processes than ever before. Together with these advances came an explosion of …

Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W **, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Docking screens for novel ligands conferring new biology: Miniperspective

JJ Irwin, BK Shoichet - Journal of medicinal chemistry, 2016 - ACS Publications
It is now plausible to dock libraries of 10 million molecules against targets over several days
or weeks. When the molecules screened are commercially available, they may be rapidly …

Emerging computational methods for the rational discovery of allosteric drugs

JR Wagner, CT Lee, JD Durrant, RD Malmstrom… - Chemical …, 2016 - ACS Publications
Allosteric drug development holds promise for delivering medicines that are more selective
and less toxic than those that target orthosteric sites. To date, the discovery of allosteric …

Folding@ home: Achievements from over 20 years of citizen science herald the exascale era

VA Voelz, VS Pande, GR Bowman - Biophysical journal, 2023 - cell.com
Simulations of biomolecules have enormous potential to inform our understanding of biology
but require extremely demanding calculations. For over 20 years, the Folding@ home …

Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity

DJ Huggins, PC Biggin, MA Dämgen… - Wiley …, 2019 - Wiley Online Library
Biomolecular simulation is increasingly central to understanding and designing biological
molecules and their interactions. Detailed, physics‐based simulation methods are …

Principles and overview of sampling methods for modeling macromolecular structure and dynamics

T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

[HTML][HTML] Protein dynamics underlying allosteric regulation

MA Astore, AS Pradhan, EH Thiede… - Current Opinion in …, 2024 - Elsevier
Allostery is the mechanism by which information and control are propagated in
biomolecules. It regulates ligand binding, chemical reactions, and conformational changes …