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cosgene: COnformation SamplinG ENginE 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.
(Fukunishi, Y., Mikami, Y., Nakamura, H. (2003) J. Phys. Chem. B. 107, 13201-13210)
Last update on Nov 10, 2015
psygene-G: Protein dYnamics SimulatinG ENginE A rapid molecular dynamics simulation program, which uses our original non-Ewald algorithm (Zero-Dipole summation method ) for electrostatic interactions, has been developed for a single and multiple GPUs (Graphics Processing Units) with the space decomposition algorithm.
Last update: 2014 January. (Mashimo, T., Fukunishi, Y., Kamiya, N., Takano, Y., Fukuda, I., Nakamura, H. (2013) J. Chem. Theory Comput. 9, 5599-5609)
Last update on Nov 10, 2015
sievgene: SIEVinG ENginE 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 1 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.
(Fukunishi, Y., Mikami, Y., Nakamura, H. (2005) J. Mol. Graph. Model. 24, 34-45)
Last update on Nov 10, 2015
sievgeneDIAV: SIEVinG ENginE with DIAV method A protein-compound docking program, sievgene, with DIAV method to estimate protein-compound binding free energy more correctly than the original sievgene does (less than about 1.3 kcal/mol).
Last update: 2013 December. (Fukunishi, Y., Nakamura, H. (2013) Pharmaceuticals 6, 604-622)
Last update on Nov 10, 2015
sievgeneNMR: SIEVinG ENginE for NMR A protein-compound docking program for prediction of protein-ligand complex structure with using NMR signal of ligand. The prediction accuracy is improved approximately twice comparing to the original sievgene by using the DIRECTION NMR signal of ligand. (Fukunishi, Y., Mizukoshi, Y., Takeuchi, K., Shimada, I., Takahashi, H., Nakamura, H. (2012) J. Mol. Graph. Model. 31, 20-27) Last update on Nov 10, 2015
sievgeneMVO: SIEVinG ENginE for Maximum Volume Overlap A protein-compound docking program for prediction of protein-ligand complex structure / drug screening with using a given known-ligand docking pose. This software performs a ligand docking and overlapping the ligand onto the given known-ligand structure given by the user at the same time. It is a combination of docking and similarity search. (Fukunishi, Y., Nakamura, H. (2012) Pharmaceuticals 5, 1332-1345) Last update on Nov 10, 2015
tplgeneX: ToPoLogy generatinG ENginE eXtended This engine is for generating molecular topologies of biological macromolecules for usage in other programs in myPresto, and it is an extended verion of the previous tplgene. A new option to parse and ouput PDBx/mmCIF format files is available. Last update on Dec 11, 2015
tplgeneL: ToPoLogy generatinG ENginE for Ligands This engine is for generating molecular topology of a target ligand (chemical compound) for usage in other programs in myPresto. Last update on Nov 10, 2015
selectMTS: Multiple Target Screening method (included in screening_packYYMMDD.tar.gz) 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. (Y. Fukunishi, Y. Mikami, S. Kubota, H. Nakamura, “Multiple target screening method for robust and accurate in silico screening.” Journal of Molecular Graphics and Modelling,25, 61-70 (2005); Y. Fukunishi, S. Kubota, H. Nakamura, “Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening”, Journal of Chemical Information and Modeling, 46, 2071-2084 (2006)) Last update on Nov 10, 2015
selectDSI: Docking Score Index method (included in screening_packYYMMDD.tar.gz) 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. (Y. Fukunishi, Y. Mikami, K. Takedomi, M. Yamanouchi, H. Shima, H. Nakamura. “Classification of chemical compounds by protein-compound docking for use in designing a focused library”, Journal of Medicinal Chemistry, 49, 523-533 (2006); Y. Fukunishi, S. Hojo, H.Nakamura, “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.”, Journal of chemical information and modeling, 46, 2610-22 (2006)) Last update on Nov 10, 2015
Hgene: Hydrogen Generation ENginE 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. Last update on Nov 10, 2015
Confgene:Conformer Generation ENginE (included in ToolsYYMMDD.tar.gz) A conformer generator for compound. Confgene can generate various conformers of compound. Last update on Nov 10, 2015
ConfgeneC: Conformer Generation ENginE for Cyclic part (included in ToolsYYMMDD.tar.gz) A conformer generator for cyclic part of compound. Last update on Nov 10, 2015
Substrucure_search A ligand-based drug screening program based on chemical compound structure comparison. A substructure search method based on the molecular structure by using the Ullman’s method. Last update on Nov 10, 2015
TGS: Topological Graph Search (A Similarity Search Using Molecular Topological Graphs) A similarity search method based on eigen values of molecular edge matrix. ( Y. Fukunishi, H. Nakamura. “A similarity search using molecular topological graphs”, Journal of Biomedicine and Biotechnology, Volume 2009 (2009), Article ID 231780) Last update on Nov 10, 2015
MD-MVO: Molecular-Dynamics Maximum-Volume Overlap A similarity search method based on overlap of molecular volume by molecular dynamics simulation. (Y. Fukunishi, H. Nakamura, “A new method for in-silico drug screening and similarity search using molecular-dynamics maximum-volume overlap (MD-MVO) method”, Journal of Molecular Graphics and Modelling, 2009, 27, 628-636) Last update on Nov 10, 2015
MolSite A ligand-binding site prediction. MolSite predicts ligand-binding site of target protein and its affinity by a compound docking simulation (Y. Fukunishi, H. Nakamura. “Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library.” Protein Science, in press.) Last update on Nov 10, 2015
UAP: Univeral Active Probes The universal active probe (UAP) is a set of drug-like compounds. This method can select the reliable drug-screening result among many screening results, since the hit ratio of the UAP is proportional to the hit ratio of the true active compounds (Y. Fukunishi, K. Ono, M. Orita, H. Nakamura. “Selection of in-silico drug screening result by using universal active probes (UAPs).” Journal of Chemical Information and Modeling, 2010, 50, 1233-1240) Last update on Nov 10, 2015
LogS_prediction A solubility (LogS) predictor based on molecular descriptor and salvation free energy calculation. Aggregators (frequent hitters) can be predicted based on the calculated LogS values (T. Mashimo, Y. Fukunishi, M. Orita, N. Katayama, S. Fujita, H. Nakamura. “Quantitative analysis of aggregation-solubility relationship by in-silico solubility prediction.” International Journal of High Throughput Screening, 2010:1, 99-107) Last update on Nov 10, 2015
3DdataConstruction A tool box for 3D mol2 file generation from 2D mol file. It can generate 3D compound database from a 2D chemical compound catalog. Last update on Nov 10, 2015
Affinity_fingerprint: Compound database and protein-compound affinity matrix 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.
LibMyPresto: Package of the library programs for parsing and writing PDBx/mmCIF and PDB formatted files. Library programs to parse and write either PDBx/mmCIF or PDB formatted files, with the users programs in C, f77 and f90 languages. Last updated on Nov 10, 2015
SyntheticAccessibility: Prediction of the synthetic accessibility of given compounds. This tool predicts the synthetic accessibility (SA) of given compounds based on the complexity, number of chiral centers and symmetry of the compound. The SA is shown as real number from 0 (easy) to 10 (difficult). (Y. Fukunishi, T. Kurosawa, Y. Mikami, H. Nakamura. Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases. Journal of Chemical Information and Modeling. (2014), 54 (12), 3259-3267.) Last updated on Nov 10, 2015
LigandBox: LIGANd Data Base Open and eXtensible This is an open database, containing the three-dimensional (3D) molecular structures and atomic charges of chemical compounds, which are available from industries. Some are collected from theKEGG DRUGdatabase.
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