Enhanced sampling with machine learning
Molecular dynamics (MD) enables the study of physical systems with excellent
spatiotemporal resolution but suffers from severe timescale limitations. To address this …
spatiotemporal resolution but suffers from severe timescale limitations. To address this …
RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
[HTML][HTML] Scalable molecular dynamics on CPU and GPU architectures with NAMD
NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …
Targeting androgen receptor phase separation to overcome antiandrogen resistance
Patients with castration-resistant prostate cancer inevitably acquire resistance to
antiandrogen therapies in part because of androgen receptor (AR) mutations or splice …
antiandrogen therapies in part because of androgen receptor (AR) mutations or splice …
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 …
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 …
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 …
[HTML][HTML] Computational methods in drug discovery
SP Leelananda, S Lindert - Beilstein journal of organic …, 2016 - beilstein-journals.org
The process for drug discovery and development is challenging, time consuming and
expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut …
expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut …
Ensemble docking in drug discovery
Ensemble docking corresponds to the generation of an" ensemble" of drug target
conformations in computational structure-based drug discovery, often obtained by using …
conformations in computational structure-based drug discovery, often obtained by using …
Protein–ligand binding with the coarse-grained Martini model
The detailed understanding of the binding of small molecules to proteins is the key for the
development of novel drugs or to increase the acceptance of substrates by enzymes …
development of novel drugs or to increase the acceptance of substrates by enzymes …