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 …
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 …
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 …
Defluorination Capability of l‐2‐Haloacid Dehalogenases in the HAD‐Like Hydrolase Superfamily Correlates with Active Site Compactness
PWY Chan, N Chakrabarti, C Ing, O Halgas… - …, 2022 - Wiley Online Library
Abstract l‐2‐Haloacid dehalogenases, industrially and environmentally important enzymes
that catalyse cleavage of the carbon‐halogen bond in s‐2‐halocarboxylic acids, were …
that catalyse cleavage of the carbon‐halogen bond in s‐2‐halocarboxylic acids, were …
Computational insights into binding of bisphosphates to farnesyl pyrophosphate synthase
K Ohno, K Mori, M Orita… - Current medicinal …, 2011 - ingentaconnect.com
Bisphosphonates (BPs) are the most widely used and effective treatment for osteoporosis
and Paget's disease. Non-nitrogen containing BPs (non-N-BPs), namely etidronate …
and Paget's disease. Non-nitrogen containing BPs (non-N-BPs), namely etidronate …
Haloacid dehalogenases of Rhizobium sp. and related enzymes: Catalytic properties and mechanistic analysis
Haloacid dehalogenases catalyse the cleavage of carbon− halogen bonds in halogenated
organic acids. These enzymes are of high interest due to their potential applications in …
organic acids. These enzymes are of high interest due to their potential applications in …
Marine Rhodobacteraceae l‐haloacid dehalogenase contains a novel His/Glu dyad that could activate the catalytic water
HR Novak, C Sayer, MN Isupov… - The FEBS …, 2013 - Wiley Online Library
The putative l‐haloacid dehalogenase gene (DehRhb) from a marine Rhodobacteraceae
family was cloned and overexpressed in Escherichia coli. The DehRhb protein was shown …
family was cloned and overexpressed in Escherichia coli. The DehRhb protein was shown …
A combined effective fragment potential–fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine …
T Nagata, DG Fedorov, T Sawada, K Kitaura… - The Journal of …, 2011 - pubs.aip.org
The gradient for the fragment molecular orbital (FMO) method interfaced with effective
fragment potentials (EFP), denoted by FMO/EFP, was developed and applied to …
fragment potentials (EFP), denoted by FMO/EFP, was developed and applied to …
The mechanistic role of active site residues in non-stereo haloacid dehalogenase E (DehE)
MHZ Abidin, KB Abd Halim, F Huyop… - Journal of Molecular …, 2019 - Elsevier
Dehalogenase E (DehE) is a non-stereospecific enzyme produced by the soil bacterium,
Rhizobium sp. RC1. Till now, the catalytic mechanism of DehE remains unclear although …
Rhizobium sp. RC1. Till now, the catalytic mechanism of DehE remains unclear although …
Multi-template homology-based structural model of L-2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1
Dehalogenases are of high interest due to their potential applications in bioremediation and
in synthesis of various industrial products. DehL is an L-2-haloacid dehalogenase (EC 3.8 …
in synthesis of various industrial products. DehL is an L-2-haloacid dehalogenase (EC 3.8 …