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 …

Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns

MJS Phipps, T Fox, CS Tautermann… - Chemical society …, 2015 - pubs.rsc.org
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 …

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 …

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 …

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

S Tanaka, Y Mochizuki, Y Komeiji, Y Okiyama… - Physical Chemistry …, 2014 - pubs.rsc.org
Recent developments in the fragment molecular orbital (FMO) method for theoretical
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 …

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 …

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 …

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 …

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 …