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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-driven drug discovery: lea** forward with confidence
Highlights•Currently, develo** a market-approved drug costs a staggering $2.6 billion.•In
silico methods have become an important strategy for narrowing down on promising lead …
silico methods have become an important strategy for narrowing down on promising lead …
Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures
The current outbreak of a novel coronavirus, named as SARS-CoV-2 causing COVID-19
occurred in 2019, is in dire need of finding potential therapeutic agents. Recently, ongoing …
occurred in 2019, is in dire need of finding potential therapeutic agents. Recently, ongoing …
[HTML][HTML] Oximes: Novel therapeutics with anticancer and anti-inflammatory potential
Oximes have been studied for decades because of their significant roles as
acetylcholinesterase reactivators. Over the last twenty years, a large number of oximes have …
acetylcholinesterase reactivators. Over the last twenty years, a large number of oximes have …
Phosphorylation-driven epichaperome assembly is a regulator of cellular adaptability and proliferation
The intricate network of protein-chaperone interactions is crucial for maintaining cellular
function. Recent discoveries have unveiled the existence of specialized chaperone …
function. Recent discoveries have unveiled the existence of specialized chaperone …
The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant
We have performed a systematic study of the entropy term in the MM/GBSA (molecular
mechanics combined with generalized Born and surface-area solvation) approach to …
mechanics combined with generalized Born and surface-area solvation) approach to …
Structure guided design of potent and selective ponatinib-based hybrid inhibitors for RIPK1
RIPK1 and RIPK3, two closely related RIPK family members, have emerged as important
regulators of pathologic cell death and inflammation. In the current work, we report that the …
regulators of pathologic cell death and inflammation. In the current work, we report that the …
MM-GB (PB) SA calculations of protein-ligand binding free energies
The importance of computational chemistry in modern scientific research is well established.
Continuous improvement in software and algorithms for the modeling of chemical …
Continuous improvement in software and algorithms for the modeling of chemical …
Toward rational design of selective molecularly imprinted polymers (MIPs) for proteins: computational and experimental studies of acrylamide based polymers for …
Molecularly imprinted polymers (MIPs) have potential as alternatives to antibodies in the
diagnosis and treatment of disease. However, atomistic level knowledge of the …
diagnosis and treatment of disease. However, atomistic level knowledge of the …
Adipocytes as anticancer drug delivery depot
Tumor-associated adipocytes promote tumor growth by providing energy and causing
chronic inflammation. Here, we have exploited the lipid metabolism to engineer adipocytes …
chronic inflammation. Here, we have exploited the lipid metabolism to engineer adipocytes …