[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 …

Emerging computational methods for the rational discovery of allosteric drugs

JR Wagner, CT Lee, JD Durrant, RD Malmstrom… - Chemical …, 2016 - ACS Publications
Allosteric drug development holds promise for delivering medicines that are more selective
and less toxic than those that target orthosteric sites. To date, the discovery of allosteric …

High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis

GM Alushin, GC Lander, EH Kellogg, R Zhang, D Baker… - Cell, 2014 - cell.com
Dynamic instability, the stochastic switching between growth and shrinkage, is essential for
microtubule function. This behavior is driven by GTP hydrolysis in the microtubule lattice and …

CageCavityCalc (C3): A Computational Tool for Calculating and Visualizing Cavities in Molecular Cages

V Martí-Centelles, TK Piskorz… - Journal of Chemical …, 2024 - ACS Publications
Organic (porous) and metal–organic cages are promising biomimetic platforms with diverse
applications spanning recognition, sensing, and catalysis. The key to the emergence of …

POVME 3.0: software for map** binding pocket flexibility

JR Wagner, J Sørensen, N Hensley… - Journal of chemical …, 2017 - ACS Publications
We present a substantial update to the open-source POVME binding pocket analysis
software. New capabilities of POVME 3.0 include a flexible chemical coloring scheme for …

How μ-opioid receptor recognizes fentanyl

QN Vo, P Mahinthichaichan, J Shen, CR Ellis - Nature communications, 2021 - nature.com
Roughly half of the drug overdose-related deaths in the United States are related to
synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor …

Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway

S Yuan, S Filipek, K Palczewski, H Vogel - Nature communications, 2014 - nature.com
Recent crystal structures of G-protein-coupled receptors (GPCRs) have revealed ordered
internal water molecules, raising questions about the functional role of those waters for …

POVME 2.0: an enhanced tool for determining pocket shape and volume characteristics

JD Durrant, L Votapka, J Sørensen… - Journal of chemical …, 2014 - ACS Publications
Analysis of macromolecular/small-molecule binding pockets can provide important insights
into molecular recognition and receptor dynamics. Since its release in 2011, the POVME …

Comprehensive insights into the catalytic mechanism of middle east respiratory syndrome 3C-like protease and severe acute respiratory syndrome 3C-like protease

H Wang, S He, W Deng, Y Zhang, G Li, J Sun… - ACS …, 2020 - ACS Publications
Coronavirus 3C-like protease (3CLPro) is a highly conserved cysteine protease employing a
catalytic dyad for its functions. 3CLPro is essential to the viral life cycle and, therefore, is an …

Full-length human GLP-1 receptor structure without orthosteric ligands

F Wu, L Yang, K Hang, M Laursen, L Wu… - Nature …, 2020 - nature.com
Abstract Glucagon-like peptide-1 receptor (GLP-1R) is a class BG protein-coupled receptor
that plays an important role in glucose homeostasis and treatment of type 2 diabetes …