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 …
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 …
Discovery of small-molecule inhibitors of the PD-1/PD-L1 axis that promote PD-L1 internalization and degradation
T Wang, S Cai, Y Cheng, W Zhang… - Journal of medicinal …, 2022 - ACS Publications
Several monoclonal antibodies targeting the programmed cell death-1/programmed cell
death-ligand 1 (PD-1/PD-L1) pathway have been used successfully in anticancer …
death-ligand 1 (PD-1/PD-L1) pathway have been used successfully in anticancer …
Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA …
With the rapid development of computational techniques and hardware, more rigorous and
precise theoretical models have been used to predict the binding affinities of a large number …
precise theoretical models have been used to predict the binding affinities of a large number …
P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape
Tyrosine kinases are regarded as excellent targets for chemical drug therapy of carcinomas.
However, under strong purifying selection, drug resistance usually occurs in the cancer cells …
However, under strong purifying selection, drug resistance usually occurs in the cancer cells …
Gasdermin E-derived caspase-3 inhibitors effectively protect mice from acute hepatic failure
Programmed cell death (PCD), including apoptosis, apoptotic necrosis, and pyroptosis, is
involved in various organ dysfunction syndromes. Recent studies have revealed that a …
involved in various organ dysfunction syndromes. Recent studies have revealed that a …
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 …
Constructing and validating high-performance MIEC-SVM models in virtual screening for kinases: a better way for actives discovery
The MIEC-SVM approach, which combines molecular interaction energy components
(MIEC) derived from free energy decomposition and support vector machine (SVM), has …
(MIEC) derived from free energy decomposition and support vector machine (SVM), has …
Bringing Structural Implications and Deep Learning-Based Drug Identification for KRAS Mutants
A Mehmood, AC Kaushik, Q Wang, CD Li… - Journal of Chemical …, 2021 - ACS Publications
Colorectal cancer is considered one of the leading causes of death that is linked with the
Kirsten Rat Sarcoma (KRAS) harboring codons 13 and 61 mutations. The objective for this …
Kirsten Rat Sarcoma (KRAS) harboring codons 13 and 61 mutations. The objective for this …