{"id":1272,"date":"2023-08-03T23:09:13","date_gmt":"2023-08-03T14:09:13","guid":{"rendered":"https:\/\/www.mypresto5.jp\/en\/?page_id=1272"},"modified":"2023-08-04T09:13:36","modified_gmt":"2023-08-04T00:13:36","slug":"how-to-cite","status":"publish","type":"page","link":"https:\/\/www.mypresto5.jp\/en\/how-to-cite\/","title":{"rendered":"How to cite"},"content":{"rendered":"\n
Program \/ Method<\/strong><\/td>References<\/strong> (Please cite the following for each program or method used.)<\/td><\/tr>
myPresto portal<\/td> IMSBIO CO., Ltd. Tokyo<\/td><\/tr>
Easy myPresto<\/td> FiatLux, Tokyo<\/td><\/tr>
myPresto General \/
cosgene \/
filling potential<\/td>		The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein-Ligand Docking
Yoshifumi Fukunishi, Yoshiaki Mikami, and Haruki Nakamura
The Journal of Physical Chemistry B 2003 107 (47), 13201-13210
DOI: 10.1021\/jp035478e<\/td><\/tr>
SRPG<\/td>The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein-Ligand Docking
Yoshifumi Fukunishi, Yoshiaki Mikami, and Haruki Nakamura
The Journal of Physical Chemistry B 2003 107 (47), 13201-13210
DOI: 10.1021\/jp035478e

Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method<\/a>
Y Fukunishi, D Mitomo, H Nakamura
Journal of chemical information and modeling 2009 49 (8), 1944-1951<\/td><\/tr>
psygene \/
psygene-G \/
zero-dipole method<\/td>		The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein-Ligand Docking
Yoshifumi Fukunishi, Yoshiaki Mikami, and Haruki Nakamura
The Journal of Physical Chemistry B 2003 107 (47), 13201-13210
DOI: 10.1021\/jp035478e

Molecular dynamics simulations accelerated by GPU for biological macromolecules with a non-Ewald scheme for electrostatic interactions<\/a>
T Mashimo, Y Fukunishi, N Kamiya, Y Takano, I Fukuda, H Nakamura
Journal of chemical theory and computation 2013 9 (12), 5599-5609<\/td><\/tr>
Receptor-ligand docking<\/td>Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening<\/a>
Y Fukunishi, Y Mikami, H Nakamura
Journal of Molecular Graphics and Modelling 2005 24 (1), 34-45<\/td><\/tr>
sievgeneNMR : Receptor-ligand docking<\/td>Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening<\/a>
Y Fukunishi, Y Mikami, H Nakamura
Journal of Molecular Graphics and Modelling 2005 24 (1), 34-45

Protein-ligand docking guided by ligand pharmacophore-mapping experiment by NMR<\/a>
Y Fukunishi, Y Mizukoshi, K Takeuchi, I Shimada, H Takahashi, H. Nakamura.
Journal of Molecular Graphics and Modelling 2011 31, 20-27<\/td><\/tr>
SBDD : Multile-target screening method<\/td>Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening<\/a>
Y Fukunishi, Y Mikami, H Nakamura
Journal of Molecular Graphics and Modelling 2005 24 (1), 34-45

Multiple target screening method for robust and accurate in silico ligand screening<\/a>
Y Fukunishi, Y Mikami, S Kubota, H Nakamura
Journal of Molecular Graphics and Modelling 2006 25 (1), 61-70

Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening
Y Fukunishi, S Kubota, H Nakamura
Journal of chemical information and modeling 2006 46 (5), 2071-2084
DOI: 10.1021\/ci060152z<\/td><\/tr>
LBDD : Doking-score index method<\/td>Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening<\/a>
Y Fukunishi, Y Mikami, H Nakamura
Journal of Molecular Graphics and Modelling 2005 24 (1), 34-45

Classification of chemical compounds by protein? compound docking for use in designing a focused library
Y Fukunishi, Y Mikami, K Takedomi, M Yamanouchi, H Shima, \u2026
Journal of Medicinal Chemistry 2006 49 (2), 523-533
DOI: 10.1021\/jm050480a

An Efficient in Silico Screening Method Based on the Protein-Compound Affinity Matrix and Its Application to the Design of a Focused Library for Cytochrome P450 (CYP) Ligands
Y Fukunishi, S Hojo, H Nakamura
Journal of chemical information and modeling 2006 46 (6), 2610-2622
DOI: 10.1021\/ci600334u<\/td><\/tr>
LigandBox<\/td>Advanced in-silico drug screening to achieve high hit ratio -Development of 3D-compound database-<\/a>
Y Fukunishi, Y Sugihara, Y Mikami, K Sakai, H Kusudo, H Nakamura
Synthesiology English edition 2009 2 (1), 64-72

LigandBox: a database for 3D structures of chemical compounds<\/a>
T Kawabata, Y Sugihara, Y Fukunishi, H Nakamura
Biophysics 2013 9, 113-121<\/td><\/tr>
MVO<\/td>A new method for in-silico drug screening and similarity search using molecular dynamics maximum volume overlap (MD-MVO) method<\/a>
Y Fukunishi, H Nakamura
Journal of Molecular Graphics and Modelling 2009 27 (5), 628-636

Prediction of protein-ligand complex structure by docking software guided by other complex structures<\/a>
Y Fukunishi, H Nakamura
Journal of Molecular Graphics and Modelling 2008 26 (6), 1030-1033<\/td><\/tr>
MolSite<\/td>Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening<\/a>
Y Fukunishi, Y Mikami, H Nakamura
Journal of Molecular Graphics and Modelling 2005 24 (1), 34-45

Prediction of ligand\u2010binding sites of proteins by molecular docking calculation for a random ligand library<\/a>
Y Fukunishi, H Nakamura
Protein Science 2010 20 (1), 95-106<\/td><\/tr>
synthetic accessibility<\/td>Prediction of synthetic accessibility based on commercially available compound databases<\/a>
Y Fukunishi, T Kurosawa, Y Mikami, H Nakamura
Journal of chemical information and modeling 2014 54 (12), 3259-3267<\/td><\/tr>
docking-score QSAR<\/td>Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening<\/a>
Y Fukunishi, Y Mikami, H Nakamura
Journal of Molecular Graphics and Modelling 2005 24 (1), 34-45

Quantitative Structure\u2010activity Relationship (QSAR) Models for Docking Score Correction<\/a>
Y Fukunishi, S Yamasaki, I Yasumatsu, K Takeuchi, T Kurosawa, Nakamura..
Molecular informatics 2016 36 (1-2), 1600013

Prediction of protein-compound binding energies from known activity data: docking\u2010score\u2010based method and its applications<\/a>
Y Fukunishi, Y Yamashita, T Mashimo, H Nakamura
Molecular Informatics 2018 37 (6-7), 1700120<\/td><\/tr>
Molecular-property prediction<\/td>Prediction of Passive Membrane Permeability by Semi\u2010Empirical Method Considering Viscous and Inertial Resistances and Different Rates of Conformational Change and Diffusion<\/a>
Y Fukunishi, T Mashimo, T Kurosawa, Y Wakabayashi, HK Nakamura, K Takeuchi.
Molecular Informatics 2019 39 (1-2), 1900071

Quantitative analysis of aggregation-solubility relationship by in-silico solubility prediction
T Mashimo, Y Fukunishi, M Orita, N Katayama, S Fujita, H Nakamura
International Journal of High Throughput Screening, 2010 99-107
DOI: 10.2147\/IJHTS.S9735<\/td><\/tr><\/tbody><\/table><\/figure>\n","protected":false},"excerpt":{"rendered":"

Program \/ Method References (Please cite the following for each program or method used.) myPresto portal IMSBIO CO., Ltd. Tokyo Easy myPresto FiatLux, Tokyo myPresto General \/cosgene \/filling potential The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein-Ligand DockingYoshifumi Fukunishi, Yoshiaki Mikami, and Haruki NakamuraThe Journal of Physical Chemistry B 2003 107 (47), 13201-13210DOI: 10.1021\/jp035478e SRPG The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein-Ligand DockingYoshifumi Fukunishi, Yoshiaki Mikami, and Haruki NakamuraThe Journal of Physical Chemistry B 2003 107 (47), 13201-13210DOI: 10.1021\/jp035478e Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) MethodY Fukunishi, D Mitomo, H NakamuraJournal…<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"tags":[],"_links":{"self":[{"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/pages\/1272"}],"collection":[{"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/comments?post=1272"}],"version-history":[{"count":4,"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/pages\/1272\/revisions"}],"predecessor-version":[{"id":1279,"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/pages\/1272\/revisions\/1279"}],"wp:attachment":[{"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/media?parent=1272"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/tags?post=1272"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}