Decision making in structure-based drug discovery: visual inspection of docking results
Molecular docking is a computational method widely used in drug discovery. Due to the
inherent inaccuracies of molecular docking, visual inspection of binding modes is a crucial …
inherent inaccuracies of molecular docking, visual inspection of binding modes is a crucial …
[HTML][HTML] Protein–ligand docking in the machine-learning era
Molecular docking plays a significant role in early-stage drug discovery, from structure-
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …
Comparative assessment of scoring functions: the CASF-2016 update
In structure-based drug design, scoring functions are often employed to evaluate protein–
ligand interactions. A variety of scoring functions have been developed so far, and thus …
ligand interactions. A variety of scoring functions have been developed so far, and thus …
Protein–ligand scoring with convolutional neural networks
Computational approaches to drug discovery can reduce the time and cost associated with
experimental assays and enable the screening of novel chemotypes. Structure-based drug …
experimental assays and enable the screening of novel chemotypes. Structure-based drug …
[HTML][HTML] Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring …
Z Wang, H Sun, X Yao, D Li, L Xu, Y Li… - Physical Chemistry …, 2016 - pubs.rsc.org
As one of the most popular computational approaches in modern structure-based drug
design, molecular docking can be used not only to identify the correct conformation of a …
design, molecular docking can be used not only to identify the correct conformation of a …
DOCK 6: Impact of new features and current docking performance
This manuscript presents the latest algorithmic and methodological developments to the
structure‐based design program DOCK 6.7 focused on an updated internal energy function …
structure‐based design program DOCK 6.7 focused on an updated internal energy function …
[HTML][HTML] Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges
IA Guedes, FSS Pereira, LE Dardenne - Frontiers in pharmacology, 2018 - frontiersin.org
Structure-based virtual screening (VS) is a widely used approach that employs the
knowledge of the three-dimensional structure of the target of interest in the design of new …
knowledge of the three-dimensional structure of the target of interest in the design of new …
Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design
PG Francoeur, T Masuda, J Sunseri, A Jia… - Journal of chemical …, 2020 - ACS Publications
One of the main challenges in drug discovery is predicting protein–ligand binding affinity.
Recently, machine learning approaches have made substantial progress on this task …
Recently, machine learning approaches have made substantial progress on this task …
[HTML][HTML] Receptor–ligand molecular docking
Docking methodology aims to predict the experimental binding modes and affinities of small
molecules within the binding site of particular receptor targets and is currently used as a …
molecules within the binding site of particular receptor targets and is currently used as a …
Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results
Our comparative assessment of scoring functions (CASF) benchmark is created to provide
an objective evaluation of current scoring functions. The key idea of CASF is to compare the …
an objective evaluation of current scoring functions. The key idea of CASF is to compare the …