Comparison of consensus scoring strategies for evaluating computational models of protein− ligand complexes
A Oda, K Tsuchida, T Takakura… - Journal of chemical …, 2006 - ACS Publications
Here, the comparisons of performance of nine consensus scoring strategies, in which multiple
scoring functions were used simultaneously to evaluate candidate structures for a protein−…
scoring functions were used simultaneously to evaluate candidate structures for a protein−…
New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models
A Oda, N Yamaotsu, S Hirono - Journal of computational …, 2005 - Wiley Online Library
The heme protein, cytochrome P450, is an oxidoreductase that plays an important role in
drug metabolism. To model P450s using molecular mechanics methods and classical …
drug metabolism. To model P450s using molecular mechanics methods and classical …
Functional characterization of wild-type and 49 CYP2D6 allelic variants for N-desmethyltamoxifen 4-hydroxylation activity
…, M Ito, C Tsukada, K Ohta, Y Endo, A Oda… - Drug metabolism and …, 2014 - jstage.jst.go.jp
Genetic variations in cytochrome P450 2D6 (CYP2D6) contribute to interindividual
variability in the metabolism of clinically used drugs, eg, tamoxifen. CYP2D6 is genetically …
variability in the metabolism of clinically used drugs, eg, tamoxifen. CYP2D6 is genetically …
Development of a novel class of tubulin inhibitor from desmosdumotin B with a hydroxylated bicyclic B-ring
K Nakagawa-Goto, A Oda, E Hamel… - Journal of medicinal …, 2015 - ACS Publications
A series of newly synthesized hydroxylated analogues of triethyldesmosdumotin B (TEDB)
with a bicyclic B-ring exhibited a significantly different mode of action for affecting microtubule …
with a bicyclic B-ring exhibited a significantly different mode of action for affecting microtubule …
[HTML][HTML] Mechanisms of deamidation of asparagine residues and effects of main-chain conformation on activation energy
K Kato, T Nakayoshi, E Kurimoto, A Oda - International Journal of …, 2020 - mdpi.com
Deamidation of asparagine (Asn) residues is a nonenzymatic post-translational modification
of proteins. Asn deamidation is associated with pathogenesis of age-related diseases and …
of proteins. Asn deamidation is associated with pathogenesis of age-related diseases and …
Functional characterization of 40 CYP3A4 variants by assessing midazolam 1′-hydroxylation and testosterone 6β-hydroxylation
…, S Tadaka, K Kinoshita, T Nakayoshi, A Oda… - Drug Metabolism and …, 2021 - ASPET
CYP3A4 is among the most abundant liver and intestinal drug-metabolizing cytochrome
P450 enzymes, contributing to the metabolism of more than 30% of clinically used drugs. …
P450 enzymes, contributing to the metabolism of more than 30% of clinically used drugs. …
Difference in substrate specificity of carboxylesterase and arylacetamide deacetylase between dogs and humans
…, T Fukami, T Kurokawa, S Gotoh, A Oda… - European Journal of …, 2018 - Elsevier
Carboxylesterase (CES) and arylacetamide deacetylase (AADAC) are the major enzymes
responsible for the hydrolysis of various clinical drugs. Our recent study demonstrated that the …
responsible for the hydrolysis of various clinical drugs. Our recent study demonstrated that the …
Functional characterization of CYP2B6 allelic variants in demethylation of antimalarial artemether
…, N Suzuki, Y Tomioka, Y Matsubara, A Oda… - Drug metabolism and …, 2011 - ASPET
Artemether (AM) is one of the most effective antimalarial drugs. The elimination half-life of
AM is very short, and it shows large interindividual variability in pharmacokinetic parameters. …
AM is very short, and it shows large interindividual variability in pharmacokinetic parameters. …
Effects of substituent pattern on the intracellular target of antiproliferative benzo [b] thiophenyl chromone derivatives
…, Y Miura, H Tsurimoto, T Nakayoshi, A Oda… - European Journal of …, 2021 - Elsevier
A new biological scaffold was produced by replacing the 6π-electron phenyl ring-B of a
natural flavone skeleton with a 10π-electron benzothiophene (BT). Since aromatic rings are …
natural flavone skeleton with a 10π-electron benzothiophene (BT). Since aromatic rings are …
Molecular dynamics simulations for the protein–ligand complex structures obtained by computational docking studies using implicit or explicit solvents
K Kato, T Nakayoshi, E Kurimoto, A Oda - Chemical Physics Letters, 2021 - Elsevier
Computational docking programs generally predict many candidates for ligand poses, and
only one or few poses should be selected for later drug design. In this study, we performed …
only one or few poses should be selected for later drug design. In this study, we performed …