End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
Kinase inhibitors: the road ahead
Receptor tyrosine kinase signalling pathways have been successfully targeted to inhibit
proliferation and angiogenesis for cancer therapy. However, kinase deregulation has been …
proliferation and angiogenesis for cancer therapy. However, kinase deregulation has been …
Protein structure-based drug design: from docking to molecular dynamics
P Śledź, A Caflisch - Current opinion in structural biology, 2018 - Elsevier
Highlights•High-throughput docking of small molecules is very successful in hit identification,
particularly for screening mainly rigid fragments.•Classical force fields with implicit solvent …
particularly for screening mainly rigid fragments.•Classical force fields with implicit solvent …
[HTML][HTML] Best practices for alchemical free energy calculations [article v1. 0]
Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …
associated with the transfer of molecules from one environment to another. The hallmark of …
Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs
Z Li, X Li, YY Huang, Y Wu, R Liu… - Proceedings of the …, 2020 - National Acad Sciences
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) has become a global crisis. There is no therapeutic treatment specific for …
(SARS-CoV-2) has become a global crisis. There is no therapeutic treatment specific for …
Enhancing hit discovery in virtual screening through absolute protein–ligand binding free-energy calculations
In the hit identification stage of drug discovery, a diverse chemical space needs to be
explored to identify initial hits. Contrary to empirical scoring functions, absolute protein …
explored to identify initial hits. Contrary to empirical scoring functions, absolute protein …
Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches
Entropy effects play an important role in drug–target interactions, but the entropic
contribution to ligand-binding affinity is often neglected by end-point binding free energy …
contribution to ligand-binding affinity is often neglected by end-point binding free energy …
Scoring functions for protein-ligand binding affinity prediction using structure-based deep learning: a review
The rapid and accurate in silico prediction of protein-ligand binding free energies or binding
affinities has the potential to transform drug discovery. In recent years, there has been a …
affinities has the potential to transform drug discovery. In recent years, there has been a …
Planet: a multi-objective graph neural network model for protein–ligand binding affinity prediction
X Zhang, H Gao, H Wang, Z Chen… - Journal of Chemical …, 2023 - ACS Publications
Predicting protein–ligand binding affinity is a central issue in drug design. Various deep
learning models have been published in recent years, where many of them rely on 3D …
learning models have been published in recent years, where many of them rely on 3D …
Network-based methods for prediction of drug-target interactions
Drug-target interaction (DTI) is the basis of drug discovery. However, it is time-consuming
and costly to determine DTIs experimentally. Over the past decade, various computational …
and costly to determine DTIs experimentally. Over the past decade, various computational …