Relative binding free energy calculations in drug discovery: recent advances and practical considerations
Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …
of structure-based drug design for decades due to the putative value it would bring to the …
Advancing drug discovery through enhanced free energy calculations
Conspectus A principal goal of drug discovery project is to design molecules that can tightly
and selectively bind to the target protein receptor. Accurate prediction of protein–ligand …
and selectively bind to the target protein receptor. Accurate prediction of protein–ligand …
OPLS4: Improving force field accuracy on challenging regimes of chemical space
We report on the development and validation of the OPLS4 force field. OPLS4 builds upon
our previous work with OPLS3e to improve model accuracy on challenging regimes of drug …
our previous work with OPLS3e to improve model accuracy on challenging regimes of drug …
OPLS3e: Extending force field coverage for drug-like small molecules
Building upon the OPLS3 force field we report on an enhanced model, OPLS3e, that further
extends its coverage of medicinally relevant chemical space by addressing limitations in …
extends its coverage of medicinally relevant chemical space by addressing limitations in …
An overview of molecular modeling for drug discovery with specific illustrative examples of applications
M Aminpour, C Montemagno, JA Tuszynski - Molecules, 2019 - mdpi.com
In this paper we review the current status of high-performance computing applications in the
general area of drug discovery. We provide an introduction to the methodologies applied at …
general area of drug discovery. We provide an introduction to the methodologies applied at …
D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
Z Gaieb, S Liu, S Gathiaka, M Chiu, H Yang… - Journal of computer …, 2018 - Springer
Abstract The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from
September 2016 through February 2017. This challenge was based on a dataset of …
September 2016 through February 2017. This challenge was based on a dataset of …
Discovery of a potent and selective tyrosine kinase 2 inhibitor: TAK-279
S Leit, J Greenwood, S Carriero, S Mondal… - Journal of Medicinal …, 2023 - ACS Publications
TYK2 is a key mediator of IL12, IL23, and type I interferon signaling, and these cytokines
have been implicated in the pathogenesis of multiple inflammatory and autoimmune …
have been implicated in the pathogenesis of multiple inflammatory and autoimmune …
Overview of the SAMPL6 host–guest binding affinity prediction challenge
Accurately predicting the binding affinities of small organic molecules to biological
macromolecules can greatly accelerate drug discovery by reducing the number of …
macromolecules can greatly accelerate drug discovery by reducing the number of …
From computer-aided drug discovery to computer-driven drug discovery
Computational chemistry and structure-based design have traditionally been viewed as a
subset of tools that could aid acceleration of the drug discovery process, but were not …
subset of tools that could aid acceleration of the drug discovery process, but were not …
Prospective evaluation of free energy calculations for the prioritization of cathepsin L inhibitors
Improving the binding affinity of a chemical series by systematically probing one of its exit
vectors is a medicinal chemistry activity that can benefit from molecular modeling input …
vectors is a medicinal chemistry activity that can benefit from molecular modeling input …