Fragmentation methods: A route to accurate calculations on large systems
MS Gordon, DG Fedorov, SR Pruitt… - Chemical …, 2012 - ACS Publications
Theoretical chemists have always strived to perform quantum mechanics (QM) calculations
on larger and larger molecules and molecular systems, as well as condensed phase …
on larger and larger molecules and molecular systems, as well as condensed phase …
Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns
The partitioning of the energy in ab initio quantum mechanical calculations into its chemical
origins (eg, electrostatics, exchange–repulsion, polarization, and charge transfer) is a …
origins (eg, electrostatics, exchange–repulsion, polarization, and charge transfer) is a …
The retinoid X receptors and their ligands
MI Dawson, Z Xia - Biochimica et Biophysica Acta (BBA)-Molecular and …, 2012 - Elsevier
This chapter presents an overview of the current status of studies on the structural and
molecular biology of the retinoid X receptor subtypes α, β, and γ (RXRs, NR2B1–3), their …
molecular biology of the retinoid X receptor subtypes α, β, and γ (RXRs, NR2B1–3), their …
Exploring chemistry with the fragment molecular orbital method
DG Fedorov, T Nagata, K Kitaura - Physical Chemistry Chemical …, 2012 - pubs.rsc.org
The fragment molecular orbital (FMO) method makes possible nearly linear scaling
calculations of large molecular systems, such as water clusters, proteins and DNA. In …
calculations of large molecular systems, such as water clusters, proteins and DNA. In …
Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems
Recent developments in the fragment molecular orbital (FMO) method for theoretical
formulation, implementation, and application to nano and biomolecular systems are …
formulation, implementation, and application to nano and biomolecular systems are …
Theoretical study of the prion protein based on the fragment molecular orbital method
T Ishikawa, T Ishikura, K Kuwata - Journal of computational …, 2009 - Wiley Online Library
We performed fragment molecular orbital (FMO) calculations to examine the molecular
interactions between the prion protein (PrP) and GN8, which is a potential curative agent for …
interactions between the prion protein (PrP) and GN8, which is a potential curative agent for …
Fragment molecular orbital calculation using the RI-MP2 method
T Ishikawa, K Kuwata - Chemical Physics Letters, 2009 - Elsevier
The resolution of the identity second-order Møller–Plesset perturbation theory (RI-MP2) was
introduced into the fragment molecular orbital (FMO) method, where the program of the RI …
introduced into the fragment molecular orbital (FMO) method, where the program of the RI …
Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles
SJ Park, I Kufareva, R Abagyan - Journal of computer-aided molecular …, 2010 - Springer
Nuclear receptors (NRs) are ligand dependent transcriptional factors and play a key role in
reproduction, development, and homeostasis of organism. NRs are potential targets for …
reproduction, development, and homeostasis of organism. NRs are potential targets for …
Covalent bond fragmentation suitable to describe solids in the fragment molecular orbital method
DG Fedorov, JH Jensen, RC Deka… - The Journal of Physical …, 2008 - ACS Publications
To improve the accuracy of the fragment molecular orbital method (FMO), we introduce a
new fragmentation scheme based on using frozen orbitals to describe fractioned bonds. By …
new fragmentation scheme based on using frozen orbitals to describe fractioned bonds. By …
Three-and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design
C Watanabe, K Fukuzawa, Y Okiyama… - Journal of Molecular …, 2013 - Elsevier
We develop an inter-fragment interaction energy (IFIE) analysis based on the three-and four-
body corrected fragment molecular orbital (FMO3 and FMO4) method to evaluate the …
body corrected fragment molecular orbital (FMO3 and FMO4) method to evaluate the …