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 …
Computational prediction of protein–protein binding affinities
T Siebenmorgen, M Zacharias - Wiley Interdisciplinary Reviews …, 2020 - Wiley Online Library
Protein–protein interactions form central elements of almost all cellular processes.
Knowledge of the structure of protein–protein complexes but also of the binding affinity is of …
Knowledge of the structure of protein–protein complexes but also of the binding affinity is of …
Molecular basis for redox control by the human cystine/glutamate antiporter system xc−
Cysteine plays an essential role in cellular redox homoeostasis as a key constituent of the
tripeptide glutathione (GSH). A rate limiting step in cellular GSH synthesis is the availability …
tripeptide glutathione (GSH). A rate limiting step in cellular GSH synthesis is the availability …
Identification of phytochemical inhibitors against main protease of COVID-19 using molecular modeling approaches
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a novel corona virus that
causes corona virus disease 2019 (COVID-19). The COVID-19 rapidly spread across the …
causes corona virus disease 2019 (COVID-19). The COVID-19 rapidly spread across the …
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 …
Structure-oriented engineering of amidase: modification of twisted access tunnel for efficient synthesis of 2-chloronicotinic acid
ZM Wu, F Xie, W Zheng, CF Liu, CP Lin, RC Zheng… - ACS …, 2023 - ACS Publications
Amidases are robust biocatalysts for the industrial synthesis of carboxylic acids. Amidase-
catalyzed hydrolysis of 2-chloronicotinamide is regarded as a promising route for 2 …
catalyzed hydrolysis of 2-chloronicotinamide is regarded as a promising route for 2 …
Thermodynamics and kinetics of drug-target binding by molecular simulation
S Decherchi, A Cavalli - Chemical Reviews, 2020 - ACS Publications
Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein–ligand binding affinity
K Huang, S Luo, Y Cong, S Zhong, JZH Zhang, L Duan - Nanoscale, 2020 - pubs.rsc.org
The molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) method is
constantly used to calculate the binding free energy of protein–ligand complexes, and has …
constantly used to calculate the binding free energy of protein–ligand complexes, and has …
Combined strategies in structure-based virtual screening
The identification and optimization of lead compounds are inalienable components in drug
design and discovery pipelines. As a powerful computational approach for the identification …
design and discovery pipelines. As a powerful computational approach for the identification …
Scanning the RBD-ACE2 molecular interactions in Omicron variant
The emergence of new SARS-CoV-2 variants poses a threat to the human population where
it is difficult to assess the severity of a particular variant of the virus. Spike protein and …
it is difficult to assess the severity of a particular variant of the virus. Spike protein and …