How to cite

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 Docking Yoshifumi Fukunishi, Yoshiaki Mikami, and Haruki Nakamura The Journal of Physical Chemistry B 2003 107 (47), 13201-13210 DOI: 10.1021/jp035478e
SRPG	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 Y Fukunishi, D Mitomo, H Nakamura Journal of chemical information and modeling 2009 49 (8), 1944-1951
psygene / psygene-G / zero-dipole method	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 T Mashimo, Y Fukunishi, N Kamiya, Y Takano, I Fukuda, H Nakamura Journal of chemical theory and computation 2013 9 (12), 5599-5609
Receptor-ligand docking	Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening Y Fukunishi, Y Mikami, H Nakamura Journal of Molecular Graphics and Modelling 2005 24 (1), 34-45
sievgeneNMR : Receptor-ligand docking	Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening 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 Y Fukunishi, Y Mizukoshi, K Takeuchi, I Shimada, H Takahashi, H. Nakamura. Journal of Molecular Graphics and Modelling 2011 31, 20-27
SBDD : Multile-target screening method	Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening 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 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
LBDD : Doking-score index method	Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening 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, … 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
LigandBox	Advanced in-silico drug screening to achieve high hit ratio -Development of 3D-compound database- 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 T Kawabata, Y Sugihara, Y Fukunishi, H Nakamura Biophysics 2013 9, 113-121
MVO	A new method for in-silico drug screening and similarity search using molecular dynamics maximum volume overlap (MD-MVO) method 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 Y Fukunishi, H Nakamura Journal of Molecular Graphics and Modelling 2008 26 (6), 1030-1033
MolSite	Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening Y Fukunishi, Y Mikami, H Nakamura Journal of Molecular Graphics and Modelling 2005 24 (1), 34-45 Prediction of ligand‐binding sites of proteins by molecular docking calculation for a random ligand library Y Fukunishi, H Nakamura Protein Science 2010 20 (1), 95-106
synthetic accessibility	Prediction of synthetic accessibility based on commercially available compound databases Y Fukunishi, T Kurosawa, Y Mikami, H Nakamura Journal of chemical information and modeling 2014 54 (12), 3259-3267
docking-score QSAR	Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening Y Fukunishi, Y Mikami, H Nakamura Journal of Molecular Graphics and Modelling 2005 24 (1), 34-45 Quantitative Structure‐activity Relationship (QSAR) Models for Docking Score Correction 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‐score‐based method and its applications Y Fukunishi, Y Yamashita, T Mashimo, H Nakamura Molecular Informatics 2018 37 (6-7), 1700120
Molecular-property prediction	Prediction of Passive Membrane Permeability by Semi‐Empirical Method Considering Viscous and Inertial Resistances and Different Rates of Conformational Change and Diffusion 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