The kth nearest neighbor method for estimation of entropy changes from molecular ensembles

F Fogolari, R Borelli, A Dovier… - Wiley Interdisciplinary …, 2024 - Wiley Online Library
All processes involving molecular systems entail a balance between associated enthalpic
and entropic changes. Molecular dynamics simulations of the end‐points of a process …

The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics

ALM Fischer, A Tichy, J Kokot… - Journal of Chemical …, 2024 - ACS Publications
Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular
dynamics (MD) simulations are an invaluable tool to study conformational changes in …

[HTML][HTML] Transformation of peptides to small molecules in medicinal chemistry: Challenges and opportunities

Z Han, Z Shen, J Pei, Q You, Q Zhang… - Acta Pharmaceutica Sinica …, 2024 - Elsevier
Peptides are native binders involved in numerous physiological life procedures, such as
cellular signaling, and serve as ready-made regulators of biochemical processes …

Free Energy Density of a Fluid and Its Role in Solvation and Binding

MK Gilson, T Kurtzman - Journal of Chemical Theory and …, 2024 - ACS Publications
The concept that a fluid has a position-dependent free energy density appears in the
literature but has not been fully developed or accepted. We set this concept on an …

Determining the gas-phase structures of α-helical peptides from shape, microsolvation, and intramolecular distance data

R Wu, JB Metternich, AS Kamenik, P Tiwari… - Nature …, 2023 - nature.com
Mass spectrometry is a powerful technique for the structural and functional characterization
of biomolecules. However, it remains challenging to accurately gauge the gas-phase …

Solvation Thermodynamics and its Applications in Drug Discovery

K Saravanan, RK Sistla - Computational Drug Discovery …, 2024 - Wiley Online Library
Life processes play out in the aqueous milieu. Consequently, water plays a key role in
molecular recognition. Both protein folding and protein–ligand interactions are driven by the …

Incorporating Solvation Thermodynamic Mapping in Computer-Aided Drug Design

Y Ji - 2024 - search.proquest.com
Advancements in computational techniques have revolutionized structure-based drug
design, substantially improving the efficiency and effectiveness of the drug discovery …

Determining the Gas-Phase Structures of α-Helical Peptides: Insights from Shape, Intramolecular Distance, and Microsolvation Assays

R Wu, JB Metternich, AS Kamenik, P Tiwari… - 2023 - research-collection.ethz.ch
Mass spectrometry is a powerful technique for the structural and functional characterization
of biomolecules. However, it remains challenging to accurately probe the gas-phase …