[PDF][PDF] Ensemble docking in drug discovery

RE Amaro, J Baudry, J Chodera, Ö Demir… - Biophysical journal, 2018 - cell.com
Ensemble docking corresponds to the generation of an" ensemble" of drug target
conformations in computational structure-based drug discovery, often obtained by using …

[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 …

[HTML][HTML] Scalable molecular dynamics on CPU and GPU architectures with NAMD

JC Phillips, DJ Hardy, JDC Maia, JE Stone… - The Journal of …, 2020 - pubs.aip.org
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 …

[HTML][HTML] Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease

H Su, S Yao, W Zhao, Y Zhang, J Liu, Q Shao… - Nature …, 2021 - nature.com
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 …

Targeting androgen receptor phase separation to overcome antiandrogen resistance

J Xie, H He, W Kong, Z Li, Z Gao, D Xie, L Sun… - Nature Chemical …, 2022 - nature.com
Patients with castration-resistant prostate cancer inevitably acquire resistance to
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 …

Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia

CJ Draper-Joyce, R Bhola, J Wang, A Bhattarai… - Nature, 2021 - nature.com
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 …

RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018 - ACS Publications
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 …

[HTML][HTML] Protein–ligand binding with the coarse-grained Martini model

PCT Souza, S Thallmair, P Conflitti… - Nature …, 2020 - nature.com
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 …

Multifaceted computational modeling in glycoscience

S Perez, O Makshakova - Chemical Reviews, 2022 - ACS Publications
Glycoscience assembles all the scientific disciplines involved in studying various molecules
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …