Three‐body expansion of the fragment molecular orbital method combined with density‐functional tight‐binding
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.24693
Abstract: The three‐body fragment molecular orbital (FMO3) method is formulated for density‐functional tight‐binding (DFTB). The energy, analytic gradient, and Hessian are derived in the gas phase, and the energy and analytic gradient are also derived for… read more here.
Keywords: density functional; functional tight; tight binding; molecular orbital ... See more keywords
Polarization energies in the fragment molecular orbital method
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26869
Abstract: Using isolated and polarized states of fragments, a method for computing the polarization energies in density functional theory (DFT) and density‐functional tight‐binding (DFTB) is developed in the framework of the fragment molecular orbital method. For… read more here.
Keywords: orbital method; polarization; fragment molecular; polarization energies ... See more keywords
Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26940
Abstract: 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‐fragment interaction energy (IFIE) and its pair interaction energy decomposition analysis (PIEDA).… read more here.
Keywords: interaction energy; fragment molecular; energy; protein ligand ... See more keywords
Exploring GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7465-8_8
Abstract: The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity. It is essential for an efficient structure-based drug design (SBDD) process. FMO… read more here.
Keywords: exploring gpcr; method; fmo; molecular orbital ... See more keywords
Machine learning prediction of inter-fragment interaction energies between ligand and amino-acid residues on the fragment molecular orbital calculations for Janus kinase – inhibitor complex
Sign Up to like & getrecommendations! Published in 2020 at "Chemical Physics Letters"
DOI: 10.1016/j.cplett.2020.137883
Abstract: Abstract Inter-Fragment Interaction Energies (IFIEs) obtained by Fragment Molecular Orbital (FMO) method can quantitatively measure the effective interactions between ligand and residues in protein, which are therefore useful for drug discovery. However, it has not… read more here.
Keywords: machine learning; fragment interaction; inter fragment; molecular orbital ... See more keywords
High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.0c00273
Abstract: Here, we have constructed neural network-based models that predict atomic partial charges with high accuracy at low computational cost. The models were trained by high-quality data acquired by quantum mechanics calculations using the fragment molecular… read more here.
Keywords: using fragment; high precision; charge; molecular orbital ... See more keywords
Hotspot Identification and Drug Design of Protein-Protein Interaction Modulators Using the Fragment Molecular Orbital Method
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00457
Abstract: 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. There are over 64,000 PPIs in the human… read more here.
Keywords: fmo ppi; protein protein; fragment molecular; drug ... See more keywords
Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c01177
Abstract: The analytic energy gradient of energy with respect to nuclear coordinates is derived for the fragment molecular orbital (FMO) method combined with time-dependent density functional theory (TDDFT). The response terms arising from the use of… read more here.
Keywords: theory; geometry; fragment molecular; gradient ... See more keywords
Locating minimum energy crossings of different spin states using the fragment molecular orbital method.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.9b00641
Abstract: Spin-dependent processes involving nonadiabatic transitions between electronic states with different spin multiplicities play important roles in the chemistry of complex systems. The rates of these processes can be predicted based on the molecular properties at… read more here.
Keywords: energy; different spin; method; spin ... See more keywords
Computational ab initio interaction analyses between neutralizing antibody and SARS-CoV-2 variant spike proteins using the fragment molecular orbital method
Sign Up to like & getrecommendations! Published in 2021 at "Bulletin of the Chemical Society of Japan"
DOI: 10.1246/bcsj.20210104
Abstract: The interaction energies between the receptor-binding domain of SARS-CoV-2 spike proteins and neutralizing antibody CC12.1 Fab were calculated using the fragment molecular orbital method. South Afr... read more here.
Keywords: using fragment; molecular orbital; spike proteins; neutralizing antibody ... See more keywords
Identification of Novel Natural Product Inhibitors against Matrix Metalloproteinase 9 Using Quantum Mechanical Fragment Molecular Orbital-Based Virtual Screening Methods
Sign Up to like & getrecommendations! Published in 2022 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms23084438
Abstract: Matrix metalloproteinases (MMPs) are calcium-dependent zinc-containing endopeptidases involved in multiple cellular processes. Among the MMP isoforms, MMP-9 regulates cancer invasion, rheumatoid arthritis, and osteoarthritis by degrading extracellular matrix proteins present in the tumor microenvironment and… read more here.
Keywords: product inhibitors; quantum mechanical; fragment molecular; natural product ... See more keywords