Blind prediction of solvation free energies from the SAMPL4 challenge

DL Mobley, KL Wymer, NM Lim, JP Guthrie - Journal of computer-aided …, 2014 - Springer
Here, we give an overview of the small molecule hydration portion of the SAMPL4
challenge, which focused on predicting hydration free energies for a series of 47 small …

Chemistry‐driven hit‐to‐lead optimization guided by structure‐based approaches

L Hoffer, C Muller, P Roche, X Morelli - Molecular Informatics, 2018 - Wiley Online Library
For several decades, hit identification for drug discovery has been facilitated by
developments in both fragment‐based and high‐throughput screening technologies …

β-Lactam estrogen receptor antagonists and a dual-targeting estrogen receptor/tubulin ligand

NM O'Boyle, JK Pollock, M Carr, AJS Knox… - Journal of Medicinal …, 2014 - ACS Publications
Twelve novel β-lactams were synthesized and their antiproliferative effects and binding
affinity for the predominant isoforms of the estrogen receptor (ER), ERα and ERβ, were …

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host–guest challenges

N Nishikawa, K Han, X Wu, F Tofoleanu… - Journal of computer …, 2018 - Springer
We calculate the absolute binding free energies of tetra-methylated octa-acids host–guest
systems as a part of the SAMPL6 blind challenge (receipt ID vq30p). We employed two …

Overcoming the Heuristic Nature of k-Means Clustering: Identification and Characterization of Binding Modes from Simulations of Molecular Recognition Complexes

PL Bremer, D De Boer, W Alvarado… - Journal of Chemical …, 2020 - ACS Publications
The accurate and reproducible detection and description of thermodynamic states in
computational data is a nontrivial problem, particularly when the number of states is …

[HTML][HTML] Deciphering the binding mechanism of Dexamethasone against SARS-CoV-2 Main Protease: Computational molecular modelling approach

SU Khan, T Htar - 2020 - europepmc.org
At present, there are no proven agents for the treatment of 2019 coronavirus disease
(COVID-19). The available evidence has not allowed guidelines to clearly recommend any …

Perspective on the SAMPL and D3R blind prediction challenges for physics-based free energy methods

N Tielker, L Eberlein, O Beckstein… - Free Energy Methods …, 2021 - ACS Publications
Solvation and binding thermodynamics of a drug-like molecule is quantified by the
respective free energy (FE) change that governs physical properties like log P/log D and …

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

J Lee, F Tofoleanu, FC Pickard, G König… - Journal of computer …, 2017 - Springer
Herein, we report the absolute binding free energy calculations of CBClip complexes in the
SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using …

Understanding the enzyme–ligand complex: insights from all-atom simulations of butyrylcholinesterase inhibition

W Alvarado, PL Bremer, A Choy, HN Dinh… - Journal of …, 2020 - Taylor & Francis
All-atom molecular dynamics simulations of butyrylcholinesterase (BChE) sans inhibitor and
in complex with each of 15 dialkyl phenyl phosphate derivatives were conducted to …

Absolute binding free energies for octa-acids and guests in SAMPL5: Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind …

F Tofoleanu, J Lee, FC Pickard IV, G König… - Journal of computer …, 2017 - Springer
As part of the SAMPL5 blind prediction challenge, we calculate the absolute binding free
energies of six guest molecules to an octa-acid (OAH) and to a methylated octa-acid …