Rigorous free energy simulations in virtual screening
Virtual high throughput screening (vHTS) in drug discovery is a powerful approach to identify
hits: when applied successfully, it can be much faster and cheaper than experimental high …
hits: when applied successfully, it can be much faster and cheaper than experimental high …
D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
Abstract The Drug Design Data Resource (D3R) aims to identify best practice methods for
computer aided drug design through blinded ligand pose prediction and affinity challenges …
computer aided drug design through blinded ligand pose prediction and affinity challenges …
Molecular mechanism of interactions between ACAD9 and binding partners in mitochondrial respiratory complex I assembly
The dual function protein ACAD9 catalyzes α, β-dehydrogenation of fatty acyl-CoA thioesters
in fatty acid β-oxidation and is an essential chaperone for mitochondrial respiratory complex …
in fatty acid β-oxidation and is an essential chaperone for mitochondrial respiratory complex …
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4
We describe a new template-based method for docking flexible ligands such as macrocycles
to proteins. It combines Monte-Carlo energy minimization on the manifold, a fast manifold …
to proteins. It combines Monte-Carlo energy minimization on the manifold, a fast manifold …
Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4
M Kadukova, V Chupin, S Grudinin - Journal of Computer-Aided Molecular …, 2020 - Springer
Abstract The D3R Grand Challenge 4 provided a brilliant opportunity to test macrocyclic
docking protocols on a diverse high-quality experimental data. We participated in both pose …
docking protocols on a diverse high-quality experimental data. We participated in both pose …
Correlation of cathepsin S with coronary stenosis degree, carotid thickness, blood pressure, glucose and lipid metabolism and vascular endothelial function in …
S Huang, Y Cao - Experimental and Therapeutic …, 2020 - spandidos-publications.com
Correlation of cathepsin S with coronary stenosis degree, carotid thickness, blood pressure,
glucose and lipid metabolism, and vascular endothelial function in patients with …
glucose and lipid metabolism, and vascular endothelial function in patients with …
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 …
respective free energy (FE) change that governs physical properties like log P/log D and …
Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S
Cathepsin S (CatS), a member of cysteine cathepsin proteases, has been well studied due
to its significant role in many pathological processes, including arthritis, cancer and …
to its significant role in many pathological processes, including arthritis, cancer and …
[HTML][HTML] Investigation of the Molecular Interactions of Vaccine Adjuvants: Can a Strategic Trio of Toll-like Receptor Agonists Enhance Efficacy in a Multifaceted …
CS Ozverel, E Erdag - Biomedical and Biotechnology Research …, 2024 - journals.lww.com
Background: The imperative need for effective vaccines against viral diseases has
intensified research on adjuvants to enhance immune responses. Toll-like receptor (TLR) …
intensified research on adjuvants to enhance immune responses. Toll-like receptor (TLR) …
The N34S mutation of SPINK1 may impact the kinetics of trypsinogen activation to cause early trypsin release in the pancreas
The N34S variant of the trypsin inhibitor SPINK1 is the clinically most significant risk factor
for chronic pancreatitis, but the underlying molecular mechanism could not be identified …
for chronic pancreatitis, but the underlying molecular mechanism could not be identified …