Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method
A theoretical scheme to systematically describe correlated (network-like) interactions
between molecular fragments is proposed within the framework of the fragment molecular …
between molecular fragments is proposed within the framework of the fragment molecular …
[HTML][HTML] Towards good correlation between fragment molecular orbital interaction energies and experimental IC50 for ligand binding: A case study of p38 MAP kinase
Y Sheng, H Watanabe, K Maruyama… - Computational and …, 2018 - Elsevier
We describe several procedures for the preprocessing of fragment molecular orbital (FMO)
calculations on p38 mitogen-activated protein (MAP) kinase and discuss the influence of the …
calculations on p38 mitogen-activated protein (MAP) kinase and discuss the influence of the …
Statistical correction to effective interactions in the fragment molecular orbital method
S Tanaka, C Watanabe, Y Okiyama - Chemical Physics Letters, 2013 - Elsevier
A theoretical scheme to evaluate effective, screened interactions between fragments is
proposed within the framework of the fragment molecular orbital (FMO) method. In this …
proposed within the framework of the fragment molecular orbital (FMO) method. In this …
Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems
Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD) is an ab initio molecular
dynamics method based on the Fragment Molecular Orbital method. FMO-MD is a general …
dynamics method based on the Fragment Molecular Orbital method. FMO-MD is a general …
A combined effective fragment potential–fragment molecular orbital method. I. The energy expression and initial applications
T Nagata, DG Fedorov, K Kitaura… - The Journal of chemical …, 2009 - pubs.aip.org
The effective fragment potential (EFP) method, a model potential for treating solvent effects
and other intermolecular interactions, is interfaced with an electronic structure method, the …
and other intermolecular interactions, is interfaced with an electronic structure method, the …
Interaction analysis of the native structure of prion protein with quantum chemical calculations
T Ishikawa, K Kuwata - Journal of Chemical Theory and …, 2010 - ACS Publications
We examined the solvent interaction and intramolecular interaction of the native structure of
prion protein (PrP) using quantum chemical calculations based on the fragment molecular …
prion protein (PrP) using quantum chemical calculations based on the fragment molecular …
Molecular interactions of the quinone electron acceptors QA, QB, and QC in photosystem II as studied by the fragment molecular orbital method
K Hasegawa, T Noguchi - Photosynthesis research, 2014 - Springer
Molecular interactions of the three plastoquinone electron acceptors, QA, QB, and QC, in
photosystem II (PSII) were studied by fragment molecular orbital (FMO) calculations …
photosystem II (PSII) were studied by fragment molecular orbital (FMO) calculations …
Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits)
N Taguchi, Y Mochizuki, T Nakano… - The Journal of …, 2009 - ACS Publications
We have performed a series of fragment molecular orbital (FMO) calculations for a family of
red fluorescent proteins, DsRed and mFruits. The electronic transition energies were …
red fluorescent proteins, DsRed and mFruits. The electronic transition energies were …
Roles of K151 and D180 in L‐2‐haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital …
T Nakamura, A Yamaguchi, H Kondo… - Journal of …, 2009 - Wiley Online Library
Abstract l‐2‐haloacid dehalogenase (l‐DEX) catalyzes the hydrolytic dehalogenation of l‐2‐
haloalkanoic acids to produce the corresponding d‐2‐hydroxyalkanoic acids. This enzyme …
haloalkanoic acids to produce the corresponding d‐2‐hydroxyalkanoic acids. This enzyme …
Novel quantitative structure-activity studies of HIV-1 protease inhibitors of the cyclic urea type using descriptors derived from molecular dynamics and molecular orbital …
T Yoshida, T Fujita, H Chuman - Current Computer-Aided Drug …, 2009 - ingentaconnect.com
Human immunodeficiency virus type 1 protease (HIV-1 PR) is an essential enzyme for the
replication cycle of HIV-1. HIV-1 PR inhibitors have been extensively investigated as anti …
replication cycle of HIV-1. HIV-1 PR inhibitors have been extensively investigated as anti …