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.
selectMTS: Multiple Target Screening method (included in screeningTools.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))
selectDSI: Docking Score Index method (included in screeningTools.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))
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Hgene: Hydrogen Generation ENginE (included in Tools.tar.gz)
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: 2010 Dec. Some bugs (wrong Gasteiger charge) were fixed. |
Confgene:Conformer Generation ENginE (included in Tools.tar.gz)
A conformer generator for compound. Confgene can generate various conformers of compound. |
ConfgeneC: Conformer Generation ENginE for Cyclic part (included in Tools.tar.gz)
A conformer generator for cyclic part of compound. |
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. |
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)
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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) |
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.) |
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) |
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) |
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. |
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. |
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 the KEGG DRUG database. |
Any Requests or Questions about myPresto should be sent to the CONTACT_US page |
