Fragment molecular orbital calculations for biomolecules

FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method

(2021) Daisuke Takaya et al.   Journal of Chemical Information and Modeling

Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins

(2021) Kaori Fukuzawa et al.   Journal of Chemical Information and Modeling

Proposal of novel potent inhibitors against androgen receptor based on ab initio molecular orbital calculations

(2021) Shunya Nakamura et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method

(2021) Shigenori Tanaka et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Characterising Inter-helical Interactions of G Protein-Coupled Receptors with the Fragment Molecular Orbital Method

(2020) Alexander Heifetz et al.   Journal of Chemical Theory and Computation

Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approach

(2020) Roberto Paciotti et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method

(2020) Daisuke Takaya et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

(2020) Hocheol Lim et al.   Scientific Reports

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

(2020) A. Acharya et al.   Journal of Chemical Information and Modeling

Discovery of Novel Spiroindoline Derivatives as Selective Tankyrase Inhibitors

(2019) Fumiyuki Shirai et al.   JOURNAL OF MEDICINAL CHEMISTRY

Characterising GPCR–ligand interactions using a fragment molecular orbital-based approach

(2019) Alexander Heifetz et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A 3D-QSAR Analysis of CDK2 Inhibitors Using FMO Calculations and PLS Regression

(2019) Tomoki Yoshida et al.   CHEMICAL & PHARMACEUTICAL BULLETIN

Systematic Interaction Analysis of Anti‐Human Immunodeficiency Virus Type‐1 Neutralizing Antibodies with High Mannose Glycans Using Fragment Molecular Orbital and Molecular Dynamics Methods

(2019) Miyu Kusumoto et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Fully Quantum Chemical Treatment of Chromophore–Protein Interactions in Phytochromes

(2019) Ronald González et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies

(2018) Yoshio Okiyama et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA

(2018) Shintaro Iwasaki et al.   MOLECULAR CELL

Protein Data Bank: the single global archive for 3D macromolecular structure data

(2018) et al.   NUCLEIC ACIDS RESEARCH

Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson–Boltzmann Surface Area (FMO+MM-PBSA) Approach

(2017) Chiduru Watanabe et al.   Journal of Chemical Information and Modeling

Application of the fragment molecular orbital method analysis to fragment-based drug discovery of BET (bromodomain and extra-terminal proteins) inhibitors

(2017) Motoyasu Ozawa et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

(2017) Dmitri G. Fedorov   Wiley Interdisciplinary Reviews-Computational Molecular Science

Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein–Ligand Binding in Solution

(2016) Dmitri G. Fedorov et al.   JOURNAL OF PHYSICAL CHEMISTRY A

The fragment molecular orbital method combined with density-functional tight-binding and the polarizable continuum model

(2016) Yoshio Nishimoto et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis

(2016) Uno Tagami et al.   ACS Medicinal Chemistry Letters

Novel type of virtual ligand screening on the basis of quantum-chemical calculations for protein–ligand complexes and extended clustering techniques

(2015) Ryo Kurauchi et al.   Computational and Theoretical Chemistry

Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method

(2014) Yoshio Nishimoto et al.   Journal of Chemical Theory and Computation

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems

(2014) Shigenori Tanaka et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A Minimal Implementation of the AMBER-PAICS Interface for Ab Initio FMO-QM/MM-MD Simulation

(2013) Takuya Okamoto et al.   BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN

Correlation Analyses on Binding Affinity of Sialic Acid Analogues and Anti-Influenza Drugs with Human Neuraminidase Using ab Initio MO Calculations on Their Complex Structures – LERE-QSAR Analysis (IV)

(2011) Seiji Hitaoka et al.   Journal of Chemical Information and Modeling

Energy Decomposition Analysis in Solution Based on the Fragment Molecular Orbital Method

(2011) Dmitri G. Fedorov et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Geometry Optimization of the Active Site of a Large System with the Fragment Molecular Orbital Method

(2011) Dmitri G. Fedorov et al.   Journal of Physical Chemistry Letters

Compound Design by Fragment-Linking

(2011) Osamu Ichihara et al.   Molecular Informatics

Discovery of a Novel Hsp90 Inhibitor by Fragment Linking

(2010) John J. Barker et al.   ChemMedChem

Fragment molecular orbital calculation using the RI-MP2 method

(2009) Takeshi Ishikawa et al.   CHEMICAL PHYSICS LETTERS