End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design

E Wang, H Sun, J Wang, Z Wang, H Liu… - Chemical …, 2019 - ACS Publications
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …

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 - Elsevier
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 …

GPCR activation mechanisms across classes and macro/microscales

AS Hauser, AJ Kooistra, C Munk… - Nature structural & …, 2021 - nature.com
Two-thirds of human hormones and one-third of clinical drugs activate~ 350 G-protein-
coupled receptors (GPCR) belonging to four classes: A, B1, C and F. Whereas a model of …

[PDF][PDF] KAMO: towards automated data processing for microcrystals

K Yamashita, K Hirata, M Yamamoto - … Crystallographica Section D …, 2018 - journals.iucr.org
In protein microcrystallography, radiation damage often hampers complete and high-
resolution data collection from a single crystal, even under cryogenic conditions. One …

Structures of active-state orexin receptor 2 rationalize peptide and small-molecule agonist recognition and receptor activation

C Hong, NJ Byrne, B Zamlynny, S Tummala… - Nature …, 2021 - nature.com
Abstract Narcolepsy type 1 (NT1) is a chronic neurological disorder that impairs the brain's
ability to control sleep-wake cycles. Current therapies are limited to the management of …

[PDF][PDF] ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography

K Hirata, K Yamashita, G Ueno, Y Kawano… - … Section D: Structural …, 2019 - journals.iucr.org
Owing to the development of brilliant microfocus beamlines, rapid-readout detectors and
sample changers, protein microcrystallography is rapidly becoming a popular technique for …

Diverse GPCRs exhibit conserved water networks for stabilization and activation

AJ Venkatakrishnan, AK Ma… - Proceedings of the …, 2019 - National Acad Sciences
G protein-coupled receptors (GPCRs) have evolved to recognize incredibly diverse
extracellular ligands while sharing a common architecture and structurally conserved …

Determination of the melanocortin-4 receptor structure identifies Ca2+ as a cofactor for ligand binding

J Yu, LE Gimenez, CC Hernandez, Y Wu, AH Wein… - Science, 2020 - science.org
The melanocortin-4 receptor (MC4R) is involved in energy homeostasis and is an important
drug target for syndromic obesity. We report the structure of the antagonist SHU9119-bound …

Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode

Y Shiimura, S Horita, A Hamamoto, H Asada… - Nature …, 2020 - nature.com
Ghrelin is a gastric peptide hormone with important physiological functions. The unique
feature of ghrelin is its Serine 3 acyl-modification, which is essential for ghrelin's activity …

A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution

WC Warren, TE Boggs, R Borowsky, BM Carlson… - Nature …, 2021 - nature.com
Identifying the genetic factors that underlie complex traits is central to understanding the
mechanistic underpinnings of evolution. Cave-dwelling Astyanax mexicanus populations …