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 …
Molecular dynamics simulations and novel drug discovery
X Liu, D Shi, S Zhou, H Liu, H Liu… - Expert opinion on drug …, 2018 - Taylor & Francis
Introduction: Molecular dynamics (MD) simulations can provide not only plentiful dynamical
structural information on biomacromolecules but also a wealth of energetic information …
structural information on biomacromolecules but also a wealth of energetic information …
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 …
Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols …
By using different evaluation strategies, we systemically evaluated the performance of
Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular …
Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular …
Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models
Here, we systematically investigated how the force fields and the partial charge models for
ligands affect the ranking performance of the binding free energies predicted by the …
ligands affect the ranking performance of the binding free energies predicted by the …
[HTML][HTML] The molecular mechanism of bisphenol A (BPA) as an endocrine disruptor by interacting with nuclear receptors: insights from molecular dynamics (MD) …
Bisphenol A (BPA) can interact with nuclear receptors and affect the normal function of
nuclear receptors in very low doses, which causes BPA to be one of the most controversial …
nuclear receptors in very low doses, which causes BPA to be one of the most controversial …
Discovery of novel inhibitors of BRD4 for treating prostate cancer: a comprehensive case study for considering water networks in virtual screening and drug design
H Zhong, X Wang, S Chen, Z Wang… - Journal of Medicinal …, 2023 - ACS Publications
Androgen receptor (AR) is the primary target for treating prostate cancer (PCa), which
inevitably progresses due to drug-resistant mutations. Bromodomain-containing protein 4 …
inevitably progresses due to drug-resistant mutations. Bromodomain-containing protein 4 …
Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance
Resistance to key first-line drugs is a major hurdle to achieve the global end tuberculosis
(TB) targets. A prodrug, pyrazinamide (PZA) is the only drug, effective in latent TB …
(TB) targets. A prodrug, pyrazinamide (PZA) is the only drug, effective in latent TB …
No impact of resistance-associated substitutions on the efficacy of sofosbuvir, velpatasvir, and voxilaprevir for 12 weeks in HCV DAA-experienced patients
C Sarrazin, CL Cooper, MP Manns, KR Reddy… - Journal of …, 2018 - Elsevier
Background & Aims In phase III studies, the fixed dose combination of sofosbuvir/velpatasvir/
voxilaprevir (SOF/VEL/VOX) administered for 12 weeks led to a sustained virologic response …
voxilaprevir (SOF/VEL/VOX) administered for 12 weeks led to a sustained virologic response …
Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations
How does a type II inhibitor bind to/unbind from a kinase target is still a confusing question
because the small molecule occupies both the ATP pocket and the allosteric pocket of the …
because the small molecule occupies both the ATP pocket and the allosteric pocket of the …