Improving small molecule virtual screening strategies for the next generation of therapeutics
BM Wingert, CJ Camacho - Current opinion in chemical biology, 2018 - Elsevier
The new generation of post-genomic targets, such as protein–protein interactions (PPIs),
often require new chemotypes not well represented in current compound libraries. This is …
often require new chemotypes not well represented in current compound libraries. This is …
Absolute binding free energy calculations improve enrichment of actives in virtual compound screening
We determined the effectiveness of absolute binding free energy (ABFE) calculations to
refine the selection of active compounds in virtual compound screening, a setting where the …
refine the selection of active compounds in virtual compound screening, a setting where the …
[HTML][HTML] Current advances in studying clinically relevant transporters of the solute carrier (SLC) family by connecting computational modeling and data science
Organic anion and cation transporting proteins (OATs, OATPs, and OCTs), as well as the
Multidrug and Toxin Extrusion (MATE) transporters of the Solute Carrier (SLC) family are …
Multidrug and Toxin Extrusion (MATE) transporters of the Solute Carrier (SLC) family are …
Meta-analysis reveals that absolute binding free-energy calculations approach chemical accuracy
H Fu, Y Zhou, X Jing, X Shao, W Cai - Journal of Medicinal …, 2022 - ACS Publications
Systematic and quantitative analysis of the reliability of formally exact methods that in silico
calculate absolute protein–ligand binding free energies remains lacking. Here, we provide …
calculate absolute protein–ligand binding free energies remains lacking. Here, we provide …
Taming multiple binding poses in alchemical binding free energy prediction: the β-cyclodextrin host–guest SAMPL9 blinded challenge
We apply the Alchemical Transfer Method (ATM) and a bespoke fixed partial charge force
field to the SAMPL9 bCD host–guest binding free energy prediction challenge that …
field to the SAMPL9 bCD host–guest binding free energy prediction challenge that …
Resolving the ligand-binding specificity in c-MYC G-quadruplex DNA: absolute binding free energy calculations and SPR experiment
We report the absolute binding free energy calculation and surface plasmon resonance
(SPR) experiment for ligand binding with the c-MYC G-quadruplex DNA. The unimolecular …
(SPR) experiment for ligand binding with the c-MYC G-quadruplex DNA. The unimolecular …
Potts Hamiltonian Models and Molecular Dynamics Free Energy Simulations for Predicting the Impact of Mutations on Protein Kinase Stability
Single-point mutations in kinase proteins can affect their stability and fitness, and
computational analysis of these effects can provide insights into the relationships among …
computational analysis of these effects can provide insights into the relationships among …
Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3
PCH Lam, R Abagyan, M Totrov - Journal of computer-aided molecular …, 2019 - Springer
In context of D3R Grand Challenge 3 we have investigated several ligand activity prediction
protocols that combined elements of a physics-based energy function (ICM VLS score) and …
protocols that combined elements of a physics-based energy function (ICM VLS score) and …
Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2
M Kadukova, S Grudinin - Journal of computer-aided molecular design, 2018 - Springer
Abstract The 2016 D3R Grand Challenge 2 provided an opportunity to test multiple protein–
ligand docking protocols on a set of ligands bound to farnesoid X receptor that has many …
ligand docking protocols on a set of ligands bound to farnesoid X receptor that has many …
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid
We have identified novel HIV-1 capsid inhibitors targeting the PF74 binding site. Acting as
the building block of the HIV-1 capsid core, the HIV-1 capsid protein plays an important role …
the building block of the HIV-1 capsid core, the HIV-1 capsid protein plays an important role …