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| Molecular simulation system (Free ware) |
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- myPresto®*1
myPresto is a molecular simulation system for structure-guided molecular development. myPresto consists of about 50 programs and databases. Namely, molecular dynamics simulation for proteins/DNA, protein-compound docking software, in-silico screening programs, conformer generator, file converting tools, and etc.
- For in-silico screening, chemical compound database is necessary. The compound database is available from BIRC/AIST.
- You can down load myPresto without charge from the web site of Laboratory of Protein Informatics, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University.
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About myPresto |
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- Protein-compound docking program"sievgene": sievgene is a flexible docking software for in-silico drug screening. Sievgene shows high performance with PC grid technology like Grid-MP (United Devices)/Active cluster (IBM).
- Automated multicanonical molecular dynamics (MD) & Simulated Tempering MD: high performance MD method. Several types of generalized ensemble methods are available. Especially, for protein modeling. Of course, usual canonical MD simulation can be performed. By using the filling potential method, the protein-compound binding free energy can be calculated.
- Generalized Born (GB)/accessible surface area (SA) & ASA methods
- NPT, NVT, NVE MD methods with rigid model/SHAKE
- Particle mesh Ewald(PME), Fast multipole method (FMM) for no-cutoff Coulomb interaction calculation
- General AMBER force field (GAFF) is available for general molecule.
- Tools for 2D to 3D structure file conversion are available for compound database. An automatic combinatorial compound generator (VCOL) is also available.
- In-silico screening methods: selectMTS: a structure-based drug screening program based on protein-compound affinity matrix. selectMTS can perform the multiple target screening (MTS) method, machine-learning MTS (MSM-MTS) method, direct score modification MTS (DSM-MTS) method. If active compounds of your target are known, a machine-learning MTS can show high hit ratio. selectDSI: a ligand-based drug screening program based on protein-compound affinity matrix. selectDSI can perform the docking score index (DSI) method and machine-learning DSI (ML-DSI) method. If active compounds of your target are known, a machine-learning DSI can show high hit ratio.
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Manuals of myPresto and major tools |
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| tplgene |
"tplgene"is a topology generator for proteins/DNAs. AMBER96/99, CHARMM19/22 force fields are available. |
| tplgeneL |
"tplgeneL" is a topology generator for general compound. General Amber Force Field, AMBER99 force fields are available. |
| cosgene |
"cosgene" is a molecular dynamics simulation program. "cosgene" can perform several kinds of generalized ensemble methods, like multicanonical MD (McMD)/Force Biased McMD. |
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myPresto manual (English) (This manual includes the manuals for tplgene, tplgeneL, cosgene and the related tools).
myPresto analysis manual (English) |
| sievgene |
"sievgene" is a protein-compound docking program. |
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myPresto sievgene manual (English)
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| MTS & DSI |
"MTS" is a structure-based in-silico drug screening method and "DSI" is a ligand-based in-silico drug screening method.
MTS/DSI manual(English) |
| 3Ddataconstruction |
Database generation tools. "VCOL" is a virtual combinatorial compound library generator. |
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myPresto VCOL manual(English) |
Latest versions of these manuals can be downloaded from the down load page below. |
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Down load |
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"Protein Informatics, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University"Web site
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"BIRC/AIST" Web site. |
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Authors and references of myPresto |
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| *1 Trade mark@No5022679 |
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