Accuracy and precision of binding free energy prediction for a tacrine related lead inhibitor of acetylcholinesterase with an arsenal of supercomputerized molecular …

R Dolezal - Journal of Biomolecular Structure and Dynamics, 2022 - Taylor & Francis
Nowadays, advanced computational chemistry methods offer various strategies for revealing
prospective hit structures in drug development essentially through accurate binding free …

TIES 2.0: A dual-topology open source relative binding free energy builder with web portal

MK Bieniek, AD Wade, AP Bhati, S Wan… - Journal of Chemical …, 2023 - ACS Publications
Relative binding free energy (RBFE) calculations are widely used to aid the process of drug
discovery. TIES, Thermodynamic Integration with Enhanced Sampling, is a dual-topology …

Enabling trade-offs between accuracy and computational cost: adaptive algorithms to reduce time to clinical insight

J Dakka, K Farkas-Pall… - 2018 18th IEEE/ACM …, 2018 - ieeexplore.ieee.org
The efficacy of drug treatments depends on how tightly small molecules bind to their target
proteins. Quantifying the strength of these interactions (the so calledbinding affinity') is a …

Concurrent and adaptive extreme scale binding free energy calculations

J Dakka, K Farkas-Pall, M Turilli… - 2018 IEEE 14th …, 2018 - ieeexplore.ieee.org
The efficacy of drug treatments depends on how tightly small molecules bind to their target
proteins. The rapid and accurate quantification of the strength of these interactions (as …

[PDF][PDF] Rapid, concurrent and adaptive extreme scale binding free energy calculation

J Dakka, K Farkas-Pall… - arXiv preprint arXiv …, 2018 - researchgate.net
The recently demonstrated ability to perform accurate, precise and rapid computation of
ligand binding strengths has driven interest in the use of molecular simulations for …

Practical challenges for biomedical modeling using HPC

D Wright, R Richardson, P Coveney - 2018 - discovery.ucl.ac.uk
The concept underlying precision medicine is that prevention, diagnosis and treatment of
pathologies such as cancer can be improved through an understanding of the influence of …