"myPresto (Medicinally Yielding PRotein Engineering SimulaTOr)" is a free software for Structure Guided Drug Development (SGDD). You can download "myPresto" from this web site.
[ myPrestoは、医薬品開発支援用分子シミュレーション計算ソフトおよびデータベースの集合体です。 このウェブサイトより、無償プログラムmyPresto の ダウンロードができます。]
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BIRC/AIST(Biomedicinal information research center / National institute for advanced industrial science and technology)
Supported by NEDO and METI of Japan
"myPresto" consists of about 50 software tools (cosgene, tplgene, tplgeneL, sievgene, selectMTS, selectDSI, Hgene, confgene, confgeneC, and etc.) and databases as follows.
A molecular dynamics simulation program for protein, DNA, chemical compound, protein-ligand complex. AMBER and CHARMM force fields are available. Cosgene can calculate NVE, NVT and NPT ensemble with various boundary conditions. In addition, cosgene can calculate the generalized ensemble like multicanonical ensemble. Cosgene can calculate the protein-compound binding free energy by the filling potential method. The generalized ensemble method is useful to calculate the free energy surface.
A protein-compound docking program for in-silico (virtual) drug screening and prediction of protein-ligand complex structure. Sievgene is a fast flexible docking program. On average, it can dock one compound to a target in 5 seconds with high accuracy (56% complex structures satisfy RMSD < 2A in a self-docking test) on usual PC. It is designed for PC grid computing.
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.
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.
A force-field parameter generator. Tplgene can generate topology file for protein and DNA using AMBER and CHARMM force field. It can add hydrogen atoms on molecules in PDB file. Also, tplgene can generate 3D coordinates of peptide from a set of torsion angles you indicate.
A force-field parameter generator for general chemical compound. tplgeneL can manipulate the compound in mol2 file format, GAMESS and Gaussian output files.
A file translation program. Hgene can add/remove hydrogen atoms to/from a general compound. It can generate a dominant ion form of chemical compound in water/vacuum.
A conformer generator for compound. Confgene can generate various conformers of compound.
A conformer generator for cyclic part of compound.
A tool box for 3D mol2 file generation from 2D mol file. It can generate 3D compound database from a 2D chemical compound catalog.
Our 3D chemical compound database consists of more than 10 millions compounds. Also, we prepared several sets of protein-compound affinity matrix generated by sievgene. The matrix is a matrix of docking scores of 182 proteins vs. 2 millions compounds. This database is essential to use selectMTS and selectDSI. Please contact Yoshifumi Fukunishi, phD (y-fukunishi * aist. go. jp: is the e-mail address. please replace * by @, and remove the space “ “.) to get these databases. The size of these databases is beyond the limit of FTP download, so that we distribute these databases by hard disk drive.