G protein-coupled receptors: structure-and function-based drug discovery

D Yang, Q Zhou, V Labroska, S Qin… - Signal transduction and …, 2021 - nature.com
As one of the most successful therapeutic target families, G protein-coupled receptors
(GPCRs) have experienced a transformation from random ligand screening to knowledge …

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

DG Fedorov - Wiley Interdisciplinary Reviews: Computational …, 2017 - Wiley Online Library
The physical picture of the fragment molecular orbital (FMO) method is described on the
basis of a many‐body expansion with terms describing the polarization of isolated …

Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations

B Ma, K Terayama, S Matsumoto, Y Isaka… - Journal of Chemical …, 2021 - ACS Publications
Recently, molecular generation models based on deep learning have attracted significant
attention in drug discovery. However, most existing molecular generation models have …

Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method

H Lim, A Baek, J Kim, MS Kim, J Liu, KY Nam… - Scientific reports, 2020 - nature.com
The prevalence of a novel β-coronavirus (SARS-CoV-2) was declared as a public health
emergency of international concern on 30 January 2020 and a global pandemic on 11 …

Density functional theory calculations of large systems: Interplay between fragments, observables, and computational complexity

W Dawson, A Degomme, M Stella… - Wiley …, 2022 - Wiley Online Library
In the past decade, developments of computational technology around density functional
theory (DFT) calculations have considerably increased the system sizes which can be …

Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy

K Takaba, C Watanabe, A Tokuhisa… - Journal of …, 2022 - Wiley Online Library
Fragment molecular orbital (FMO) method is a powerful computational tool for structure‐
based drug design, in which protein–ligand interactions can be described by the inter …

FMODB: The world's first database of quantum mechanical calculations for biomacromolecules based on the fragment molecular orbital method

D Takaya, C Watanabe, S Nagase… - Journal of Chemical …, 2021 - ACS Publications
We developed the world's first web-based public database for the storage, management,
and sharing of fragment molecular orbital (FMO) calculation data sets describing the …

Investigation of protein-protein interactions and hot spot region between PD-1 and PD-L1 by fragment molecular orbital method

H Lim, J Chun, X Jin, J Kim, JH Yoon, KT No - Scientific reports, 2019 - nature.com
Inhibitors to interfere protein-protein interactions (PPI) between programmed cell death 1
(PD-1) and programmed death ligand-1 (PD-L1) block evasion of cancers from immune …

New mutations in non-syndromic primary ovarian insufficiency patients identified via whole-exome sequencing

LC Patiño, I Beau, C Carlosama, JC Buitrago… - Human …, 2017 - academic.oup.com
STUDY QUESTION Is it possible to identify new mutations potentially associated with non-
syndromic primary ovarian insufficiency (POI) via whole-exome sequencing (WES) …

Hotspot identification and drug design of protein–protein interaction modulators using the fragment molecular orbital method

S Monteleone, DG Fedorov… - Journal of Chemical …, 2022 - ACS Publications
Protein–protein interactions (PPIs) are essential for the function of many proteins. Aberrant
PPIs have the potential to lead to disease, making PPIs promising targets for drug discovery …