A practical guide to large-scale docking

BJ Bender, S Gahbauer, A Luttens, J Lyu, CM Webb… - Nature protocols, 2021 - nature.com
Abstract Structure-based docking screens of large compound libraries have become
common in early drug and probe discovery. As computer efficiency has improved and …

Structure-based virtual screening for ligands of G protein–coupled receptors: what can molecular docking do for you?

F Ballante, AJ Kooistra, S Kampen, C de Graaf… - Pharmacological …, 2021 - ASPET
G protein–coupled receptors (GPCRs) constitute the largest family of membrane proteins in
the human genome and are important therapeutic targets. During the last decade, the …

[HTML][HTML] Best practices for alchemical free energy calculations [article v1. 0]

ASJS Mey, BK Allen, HEB Macdonald… - Living journal of …, 2020 - ncbi.nlm.nih.gov
Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …

Emerging diversity in lipid–protein interactions

V Corradi, BI Sejdiu, H Mesa-Galloso… - Chemical …, 2019 - ACS Publications
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable
membrane environment for proteins to being embedded in to detailed roles in complicated …

How ligands illuminate GPCR molecular pharmacology

D Wacker, RC Stevens, BL Roth - Cell, 2017 - cell.com
G protein-coupled receptors (GPCRs), which are modulated by a variety of endogenous and
synthetic ligands, represent the largest family of druggable targets in the human genome …

[HTML][HTML] Crystal structure of an LSD-bound human serotonin receptor

D Wacker, S Wang, JD McCorvy, RM Betz… - Cell, 2017 - cell.com
The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the
crystal structure of LSD in complex with the human serotonin receptor 5-HT 2B. The complex …

Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance

G Enkavi, M Javanainen, W Kulig, T Róg… - Chemical …, 2019 - ACS Publications
Biological membranes are tricky to investigate. They are complex in terms of molecular
composition and structure, functional over a wide range of time scales, and characterized by …

A method for structure determination of GPCRs in various states

Q Guo, B He, Y Zhong, H Jiao, Y Ren, Q Wang… - Nature Chemical …, 2024 - nature.com
G-protein-coupled receptors (GPCRs) are a class of integral membrane proteins that detect
environmental cues and trigger cellular responses. Deciphering the functional states of …

How were new medicines discovered?

DC Swinney, J Anthony - Nature reviews Drug discovery, 2011 - nature.com
Preclinical strategies that are used to identify potential drug candidates include target-based
screening, phenotypic screening, modification of natural substances and biologic-based …

Structure-function of the G protein–coupled receptor superfamily

V Katritch, V Cherezov… - Annual review of …, 2013 - annualreviews.org
During the past few years, crystallography of G protein–coupled receptors (GPCRs) has
experienced exponential growth, resulting in the determination of the structures of 16 distinct …