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myPresto

  • Openness:3 ★★★
  • Document quality:3 ★★★

Commercially-available free software for Computer-Aided Drug Development. It includes programs for compound database, protein-compound docking, structure-based drug screening, ligand-based drug screening, protein-ligand binding site prediction, molecular editor, physical property prediction, synthetic accessibility prediction, thermodynamic calculation including multi-canonical dynamics, and molecular dynamics simulations with and without acceleration using GPUs and MPI parallelization.

Information
Last Update:2024/12/10

Official site

https://www.mypresto5.jp/en/

License

JBCI (Japan Biological Informatics Consortium) members and myPresto developers listed in the official site (https://www.mypresto5.jp/en/license/) can use developed versions under 2-Clause BSD license (※1).

The others can use released versions distributed in the official site (https://www.mypresto5.jp/en/) under GNU Lesser GPL 2.1 (※2).

※1 2-Clause BSD License: https://opensource.org/licenses/BSD-2-Clause

※2 GNU Lesser GPL 2.1: https://opensource.org/licenses/LGPL-2.1
Availability

Linux (RedHat, CentOS, etc.), Windows7/8/8.1/10
Core Developers

Haruki Nakamura (Institute for Protein Research, Osaka University), Yoshifumi Fukunishi (National Institute for Advanced Industrial Science and Technology), Akinori Kidera  (Graduate School of Medical Life Science, Yokohama City University), Bhaskar Dasgupta (JBIC), Eiji Kanamori (Hitachi solutions, Ltd), Ikuo Fukuda (Institute for Protein Research, Osaka University), Jae-Gil Kim (JBIC), Junichi Higo (Institute for Protein Research, Osaka University), Kota Kasahara (College of Life Science, Ritsumeikan University), Mituhito Wada (Fujitsu, Co., Ltd), Narutoshi Kamiya (Graduate School of Simulation Studies, University of Hyogo), Satoru Kubota (Hitachi solutions East Japan, Ltd), Tadaaki Mashimo (IMSBio, Co., Ltd), Tohru Terada (Graduate School of Agricultutal and Life Sciences, The University of Tokyo), Yoshiaki Mikami (Hitachi solutions East Japan, Ltd), Yuichi Hashi (Hitachi solutions East Japan, Ltd)
Target substance/model

biomolecules, proteins, peptides, saccharides, small organic molecules, solutions
Physical quantities that can be computed

free energy, binding energy between proteins and small organic molecules, solubility
Methodology

molecular dynamics, drug docking/screening, molecular similarity comparison, regression analysis, principal component analysis
Parallelization

Molecular dynamics simulation using a cosgene/psygene module supports MPI parallelization. Molecular dynamics simulation using a psygene-G/omegagene module supports CUDA parallelization (GPU parallelization).
Document

Cosgene MD simulation:
Y. Fukunishi, Y. Mikami, H. Nakamura. J. Phys. Chem. B. 107, 13201-13210 (2003).

Psygene-G MD simulation on GPU:
T. Mashimo, Y. Fukunishi, N. Kamiya, Y. Takano, I. Fukuda, H. Nakamura. J. Chem. Theory Comput.9, 5599-5609 (2013).
J. Higo, B. Dasgupta, T. Mashimo, K. Kasahara,Y. Fukunishi, H. Nakamura J. Comput. Chem. 36, 1489-1501 (2015).
N. Kamiya, T. Mashimo, Y. Takano, T. Kon, G. Kurisu, H. Nakamura, Protein Engineering, Design and Selection, 29, 317-326 (2016).

Omegagene MD simulation on GPU:
K. Kasahara, B. Ma, K. Goto, B. Dasgupta, J. Higo, I. Fukuda, T. Mashimo, Y. Akiyama, H. Nakamura, Biophysics and Physicobiology, in press.

Sivgene protein-ligand docking:
Y. Fukunishi, Y. Mikami, H. Nakamura. J. Mol. Graph. Model. 24, 34-45 (2005).

Sievgene NMR protein-ligand docking by NMR experimental data:
Y. Fukunishi, Y. Mizukoshi, K. Takeuchi, I. Shimada, H. Takahashi, H. Nakamura. J. Mol. Graph. Model. 31, 20-27 (2012).

Structure-based drug screening:
Y. Fukunishi, Y. Mikami, S. Kubota, H. Nakamura. J. Mol. Graph. Model. 25, 61-70 (2005).
Y. Fukunishi, S. Kubota, H. Nakamura. J. Chem. Inf. Model. 46, 2071-2084 (2006).

Ligand-based drug screening:
Y. Fukunishi, Y. Mikami, K. Takedomi, M. Yamanouchi, H. Shima, H. Nakamura. J. Med. Chem. 49, 523-533 (2006).
Y. Fukunishi, S. Hojo, H. Nakamura. J. Chem. Inf. Model. 46, 2610-2622 (2006).

Solubility prediction:
T. Mashimo, Y. Fukunishi, M. Orita, N. Katayama, S. Fujita, H. Nakamura. International Journal of High Throughput Screening, 2010:1, 99-107 (2010).

Synthetic accessibility prediction:
Y. Fukunishi, T. Kurosawa, Y. Mikami, H. Nakamura. J. Chem. Inf. Model. 54, 3259-3267 (2014).
Other

myPresto provides both the Structure-Based Drug Development and the Ligand-Based Drug Development environments. The users can perform from hit screening to lead-generation in one program suit, since this suit provides from compound database for screening to MD simulation for compound detail validation. myPresto has been developed and opened since 2000, and it will be available to the future.

MPI/MPICH is needed for parallelized version of molecular dynamics (cosgene-MPI, psygene).
CUDA is needed for molecular dynamics simulation on GPUs (psygene-G/omeggagene).

The following commercial software supports GUI operation of myPresto on Linux/Windows/Mac.

MolDesk: http://www.moldesk.com/en/
MF myPresto: http://www.fiatlux.co.jp/product/lifescience/MFMYPRESTO/MFmyPresto-index.html(in Japanese)

The following database provides data of compounds in the myPresto format.

LigandBox: http://www.moldesk.net/ligandbox/cgi-bin/index.cgi?LANG=en
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