Calculate protein–ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3
We participated in the Cathepsin S (CatS) sub-challenge of the Drug Design Data Resource
(D3R) Grand Challenge 3 (GC3) in 2017 to blindly predict the binding poses of 24 CatS …
(D3R) Grand Challenge 3 (GC3) in 2017 to blindly predict the binding poses of 24 CatS …
Blinded prediction of protein–ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4
J Zou, C Tian, C Simmerling - Journal of computer-aided molecular design, 2019 - Springer
In the framework of the 2018 Drug Design Data Resource grand challenge 4, blinded
predictions on relative binding free energy were performed for a set of 39 ligands of the …
predictions on relative binding free energy were performed for a set of 39 ligands of the …
D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings
Abstract The Drug Design Data Resource aims to test and advance the state of the art in
protein–ligand modeling by holding community-wide blinded, prediction challenges. Here …
protein–ligand modeling by holding community-wide blinded, prediction challenges. Here …
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 …
Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3
PI Koukos, LC Xue, AMJJ Bonvin - Journal of computer-aided molecular …, 2019 - Springer
We report the performance of HADDOCK in the 2018 iteration of the Grand Challenge
organised by the D3R consortium. Building on the findings of our participation in last year's …
organised by the D3R consortium. Building on the findings of our participation in last year's …
Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations
During the last few years, we have developed a docking protocol involving two steps:(i) the
choice of the most appropriate docking software and parameters for the system of interest …
choice of the most appropriate docking software and parameters for the system of interest …
Prediction of binding free energy of protein–ligand complexes with a hybrid molecular mechanics/generalized born surface area and machine learning method
L Dong, X Qu, Y Zhao, B Wang - ACS omega, 2021 - ACS Publications
Accurate prediction of protein–ligand binding free energies is important in enzyme
engineering and drug discovery. The molecular mechanics/generalized Born surface area …
engineering and drug discovery. The molecular mechanics/generalized Born surface area …
Improving the accuracy of predicting protein–ligand binding-free energy with semiempirical quantum chemistry charge
Aim: It is a challenge to predict binding-free energy (Δ G) accurately. Methodology/results:
For accurate Δ G prediction, a new strategy combining solvated interaction energy (SIE) or …
For accurate Δ G prediction, a new strategy combining solvated interaction energy (SIE) or …
BFEE: A user-friendly graphical interface facilitating absolute binding free-energy calculations
Quantifying protein–ligand binding has attracted the attention of both theorists and
experimentalists for decades. Many methods for estimating binding free energies in silico …
experimentalists for decades. Many methods for estimating binding free energies in silico …
Combined linear interaction energy and alchemical solvation free-energy approach for protein-binding affinity computation
Calculating free energies of binding (Δ G bind) between ligands and their target protein is of
major interest to drug discovery and safety, yet it is still associated with several challenges …
major interest to drug discovery and safety, yet it is still associated with several challenges …