User profiles for Tomoshi Kameda
Tomoshi Kameda産業技術総合研究所 人工知能研究センター Verified email at aist.go.jp Cited by 1758 |
On easy implementation of a variant of the replica exchange with solute tempering in GROMACS
T Terakawa, T Kameda… - Journal of computational …, 2011 - Wiley Online Library
To reduce the number of replicas required in the conventional replica exchange method for
huge systems, recently the replica exchange with solute tempering (REST) method was …
huge systems, recently the replica exchange with solute tempering (REST) method was …
Machine-learning-guided mutagenesis for directed evolution of fluorescent proteins
…, M Oikawa, H Nakazawa, T Niide, T Kameda… - ACS synthetic …, 2018 - ACS Publications
Molecular evolution based on mutagenesis is widely used in protein engineering. However,
optimal proteins are often difficult to obtain due to a large sequence space. Here, we …
optimal proteins are often difficult to obtain due to a large sequence space. Here, we …
[HTML][HTML] Liquid-like droplet formation by tumor suppressor p53 induced by multivalent electrostatic interactions between two disordered domains
Early in vivo studies demonstrated the involvement of a tumor-suppressing transcription
factor, p53, into cellular droplets such as Cajal and promyelocytic leukemia protein bodies, …
factor, p53, into cellular droplets such as Cajal and promyelocytic leukemia protein bodies, …
Arginine-assisted solubilization system for drug substances: solubility experiment and simulation
The poor aqueous solubility of drug substances hampers their broader applications. This paper
describes a de novo strategy to increase the aqueous solubility of drug substances using …
describes a de novo strategy to increase the aqueous solubility of drug substances using …
Machine-learning-guided library design cycle for directed evolution of enzymes: the effects of training data composition on sequence space exploration
…, M Oikawa, T Sato, H Nakazawa, T Ito, T Kameda… - Acs …, 2021 - ACS Publications
Machine learning (ML) is becoming an attractive tool in mutagenesis-based protein
engineering because of its ability to design a variant library containing proteins with a desired …
engineering because of its ability to design a variant library containing proteins with a desired …
Pressure and temperature phase diagram for liquid–liquid phase separation of the RNA-binding protein fused in sarcoma
…, R Yamazaki, A Fujiwara, T Kameda… - The Journal of …, 2021 - ACS Publications
Liquid–liquid phase separation (LLPS) of proteins and nucleic acids to form membraneless
cellular compartments is considered to be involved in various biological functions. The RNA-…
cellular compartments is considered to be involved in various biological functions. The RNA-…
Aromaphilicity Index of Amino Acids: Molecular Dynamics Simulations of the Protein Binding Affinity for Carbon Nanomaterials
Aromatic carbon nanomaterials, such as carbon nanotubes and graphene, undergo protein
adsorption in the early stages of their uptake into biological systems, which determines their …
adsorption in the early stages of their uptake into biological systems, which determines their …
[HTML][HTML] Comprehensive prediction of lncRNA–RNA interactions in human transcriptome
Motivation Recent studies have revealed that large numbers of non-coding RNAs are
transcribed in humans, but only a few of them have been identified with their functions. …
transcribed in humans, but only a few of them have been identified with their functions. …
Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules
S Iida, K Tomoshi - Biophysical Reviews, 2022 - Springer
Non-equilibrium molecular dynamics (NEMD) simulation has been recognized as a
powerful tool for examining biomolecules and provides fruitful insights into not only non-equilibrium …
powerful tool for examining biomolecules and provides fruitful insights into not only non-equilibrium …
A covalent G-site inhibitor for glutathione S-transferase Pi (GSTP 1-1)
…, Y Sekido, Y Murakami-Tonami, T Kameda… - Chemical …, 2017 - pubs.rsc.org
We herein report the first covalent G-site-binding inhibitor for GST, GS-ESF (1), which
irreversibly inhibited the GSTP1-1 function. LC-MS/MS and X-ray structure analyses of the …
irreversibly inhibited the GSTP1-1 function. LC-MS/MS and X-ray structure analyses of the …