Gaussian accelerated molecular dynamics: Principles and applications
Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for
simultaneous unconstrained enhanced sampling and free energy calculations of …
simultaneous unconstrained enhanced sampling and free energy calculations of …
Predicting biomolecular binding kinetics: A review
Biomolecular binding kinetics including the association (k on) and dissociation (k off) rates
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …
[HTML][HTML] Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease
The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently needs an effective cure. 3CL …
respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently needs an effective cure. 3CL …
Decoding the identification mechanism of an SAM-III Riboswitch on ligands through multiple independent Gaussian-accelerated molecular dynamics simulations
J Chen, Q Zeng, W Wang, H Sun… - Journal of Chemical …, 2022 - ACS Publications
S-Adenosyl-l-methionine (SAM)-responsive riboswitches play a central role in the regulation
of bacterial gene expression at the level of transcription attenuation or translation inhibition …
of bacterial gene expression at the level of transcription attenuation or translation inhibition …
Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia
The adenosine A1 receptor (A1R) is a promising therapeutic target for non-opioid analgesic
agents to treat neuropathic pain,. However, development of analgesic orthosteric A1R …
agents to treat neuropathic pain,. However, development of analgesic orthosteric A1R …
CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
CRISPR-Cas9 has become a facile genome editing technology, yet the structural and
mechanistic features underlying its function are unclear. Here, we perform extensive …
mechanistic features underlying its function are unclear. Here, we perform extensive …
[HTML][HTML] A unified resource for tracking anti-CRISPR names
Dear editors In the battle between CRISPR-Cas* prokaryotic immune systems and the
elements that they target, a diverse array of ''anti-CRISPR''proteins have evolved. These …
elements that they target, a diverse array of ''anti-CRISPR''proteins have evolved. These …
Multi-state model-based identification of cryptic allosteric sites on human serotonin transporter
G Tu, B Xu, D Luo, J Liu, Z Liu, G Chen… - ACS Chemical …, 2023 - ACS Publications
Serotonin transporter (SERT) plays a fundamental role in taking the synaptic cleft serotonin
back to the presynaptic neuron. The discovery of allosteric SERT modulators represents the …
back to the presynaptic neuron. The discovery of allosteric SERT modulators represents the …
Time evolution of the millisecond allosteric activation of imidazole glycerol phosphate synthase
C Calvó-Tusell, MA Maria-Solano… - Journal of the …, 2022 - ACS Publications
Deciphering the molecular mechanisms of enzymatic allosteric regulation requires the
structural characterization of functional states and also their time evolution toward the …
structural characterization of functional states and also their time evolution toward the …
Allosteric motions of the CRISPR–Cas9 HNH nuclease probed by NMR and molecular dynamics
KW East, JC Newton, UN Morzan… - Journal of the …, 2019 - ACS Publications
CRISPR–Cas9 is a widely employed genome-editing tool with functionality reliant on the
ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA …
ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA …