{"id":15,"date":"2017-12-18T21:58:16","date_gmt":"2017-12-18T12:58:16","guid":{"rendered":"http:\/\/mypresto5.jp\/en\/?page_id=15"},"modified":"2026-02-05T01:27:47","modified_gmt":"2026-02-04T16:27:47","slug":"top","status":"publish","type":"page","link":"https:\/\/www.mypresto5.jp\/en\/","title":{"rendered":"Top"},"content":{"rendered":"<p><a href=\"https:\/\/www.mypresto5.jp\/en\/downloads\/\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-147\" src=\"https:\/\/www.mypresto5.jp\/en\/wp-content\/uploads\/2017\/12\/download.png\" alt=\"\" width=\"220\" height=\"60\" \/><\/a>\u00a0 \u00a0 \u00a0 \u00a0<a href=\"https:\/\/www.mypresto5.jp\/en\/wp-content\/uploads\/2018\/09\/user_manual_v5.000_en_180926.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">User Manual v5.000<\/a><\/p>\n<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_80 counter-hierarchy ez-toc-counter ez-toc-light-blue ez-toc-container-direction\">\n<p class=\"ez-toc-title\" style=\"cursor:inherit\">Table of Contents<\/p>\n<label for=\"ez-toc-cssicon-toggle-item-69d7729217e83\" class=\"ez-toc-cssicon-toggle-label\"><span class=\"\"><span class=\"eztoc-hide\" style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #999;color:#999\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewBox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #999;color:#999\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewBox=\"0 0 24 24\" version=\"1.2\" baseProfile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/label><input type=\"checkbox\"  id=\"ez-toc-cssicon-toggle-item-69d7729217e83\"  aria-label=\"Toggle\" \/><nav><ul class='ez-toc-list ez-toc-list-level-1 ' ><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/www.mypresto5.jp\/en\/#Simple_software_package_with_graphic_interface\" >Simple software package with graphic interface<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-2\" href=\"https:\/\/www.mypresto5.jp\/en\/#Molecular_dynamics_simulation\" >Molecular dynamics simulation<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-3\" href=\"https:\/\/www.mypresto5.jp\/en\/#Structure_preparation_and_file_format_conversion_for_small_molecules_etc\" >Structure preparation and file format conversion for small molecules, etc.<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-4\" href=\"https:\/\/www.mypresto5.jp\/en\/#Force-field_parameter_assignment\" >Force-field parameter assignment<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-5\" href=\"https:\/\/www.mypresto5.jp\/en\/#Membrane_system\" >Membrane system<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-6\" href=\"https:\/\/www.mypresto5.jp\/en\/#Free_energy_calculation\" >Free energy calculation<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-7\" href=\"https:\/\/www.mypresto5.jp\/en\/#Conformer_generation\" >Conformer generation<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-8\" href=\"https:\/\/www.mypresto5.jp\/en\/#Compound_database\" >Compound database<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-9\" href=\"https:\/\/www.mypresto5.jp\/en\/#Receptor-ligand_binding_site_search\" >Receptor-ligand binding site search<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-10\" href=\"https:\/\/www.mypresto5.jp\/en\/#Protein-compound_docking\" >Protein-compound docking<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-11\" href=\"https:\/\/www.mypresto5.jp\/en\/#in-silico_drug_screening\" >in-silico drug screening<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-12\" href=\"https:\/\/www.mypresto5.jp\/en\/#Physical_property_estimation\" >Physical property estimation<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-13\" href=\"https:\/\/www.mypresto5.jp\/en\/#Synthetic_accessibility_estimation_and_Drug_design\" >Synthetic accessibility estimation and Drug design<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-1'><a class=\"ez-toc-link ez-toc-heading-14\" href=\"https:\/\/www.mypresto5.jp\/en\/#Interface_for_new_PDB_format\" >Interface for new PDB format<\/a><\/li><\/ul><\/nav><\/div>\n<h1><span class=\"ez-toc-section\" id=\"Simple_software_package_with_graphic_interface\"><\/span>Simple software package with graphic interface<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<table style=\"border-collapse: collapse; width: 100%;\">\n<tbody>\n<tr>\n<td style=\"width: 50%;\">\n<h3>myPresto Portal<\/h3>\n<p><img decoding=\"async\" src=\"https:\/\/www.mypresto5.jp\/en\/wp-content\/uploads\/2022\/09\/mypresto_portal.gif\" \/><\/p>\n<p>myPresto Protal is a graphic user interface (GUI) program for myPresto and GROMACS, available for Windows, MAC and Linux (all 64bit).<br \/>\n<span style=\"color: #ff0000;\">Last updated on February 4<\/span><span style=\"color: #ff0000;\">, 2026<\/span><\/p>\n<p><a href=\"https:\/\/www.mypresto5.jp\/en\/wp-content\/uploads\/2026\/02\/myPresto_Portal_ver.1.1_QuickManual_en.pdf\">myPresto Portal Quick Manual<\/a><\/td>\n<td style=\"width: 50%;\">\n<h3>Easy myPresto<\/h3>\n<p><img decoding=\"async\" src=\"https:\/\/www.mypresto5.jp\/en\/wp-content\/uploads\/2022\/09\/Easy_myPresto.png\" \/><\/p>\n<p>Easy myPresto is a graphic user interface (GUI) program for myPresto, available for Windows, MAC and Linux (all 64bit).<br \/>\n<span style=\"color: #ff0000;\">Last updated on January 11, 2024<\/span><\/p>\n<p><a href=\"https:\/\/www.fiatlux.co.jp\/users\/easymypresto\/Document\/UsersGuide\/index.html\">Easy myPresto Manual (Japanese)<\/a><\/td>\n<\/tr>\n<tr>\n<td colspan=\"2\"><span style=\"color: #ff0000;\">The free version is distributed through the generosity of member companies, with restrictions on molecular weight, functions, etc., to paid software.<\/span><\/td>\n<\/tr>\n<tr>\n<td><a href=\"https:\/\/moldesk.stores.jp\/\">MolDesk EC shop<\/a><\/td>\n<td><a href=\"https:\/\/www.fiatlux.co.jp\/product\/lifescience\/mfmypresto\/index.html\">Paid version of Easy myPresto<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h1><span class=\"ez-toc-section\" id=\"Molecular_dynamics_simulation\"><\/span>Molecular dynamics simulation<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>cosgene: COnformation SamplinG ENginE<\/h3>\n<p>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.<br \/>\n<em>Fukunishi, Y., Mikami, Y., Nakamura, H. (2003) J. Phys. Chem. B. 107, 13201-13210<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on February 23, 2020<\/span><\/p>\n<h3>psygene-G: Protein dYnamics SimulatinG ENginE for GPU<\/h3>\n<p>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.<br \/>\n<em>Mashimo, T., Fukunishi, Y., Kamiya, N., Takano, Y., Fukuda, I., Nakamura, H. (2013) J. Chem. Theory Comput. 9, 5599-5609<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on November 7, 2019<\/span><\/p>\n<h3>omegagene: a GPU-accelerated molecular dynamics simulator with enhanced conformational sampling<\/h3>\n<p>A new engine, \u201comegagene\u201d, has joined in myPresto program suits for more effective conformational sampling with GPU-accelerated molecular dynamics simulation. It incorporates our original non-Ewald algorithm, Zero-Multipole summation Method (ZMM), and an improved Multicanonical molecular dynamics (v-McMD) algorithm. This program has been developed mainly at Osaka University, and it is also distributed under Open-Source License from\u00a0<a href=\"http:\/\/www.protein.osaka-u.ac.jp\/rcsfp\/pi\/omegagene\/\">http:\/\/www.protein.osaka-u.ac.jp\/rcsfp\/pi\/omegagene\/<\/a>.<br \/>\n<em>Kasahara, K., Ma, B., Goto, K., Dasgupta, B., Higo, J., Fukuda, I., Mashimo, T., Akiyama, Y., Nakamura, H. (2016) Biophys. &amp; Physicobiol. 13, 209-216: DOI 10.2142\/biophysico.13.0_209<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on January 14, 2018<\/span><\/p>\n<h3>PDBcheck<\/h3>\n<p>Checks the validity of input PDB files, determines N- and C-terminal modifications and disulfide bonds (S-S) of proteins, and edits H-amino acid states of metal-binding sites.<\/p>\n<h3>setwater<\/h3>\n<p>Add solvent water molecules to systems containing proteins, DNA\/RNA, membranes, and small molecules in spherical (isolated) and rectangular (periodic) forms.<\/p>\n<h3>add_ion<\/h3>\n<p>Neutralizes the charge with NaCl at a specified concentration and adjusts the salt concentration to an arbitrary level for isolated and periodic systems hydrated with setwater containing proteins, DNA\/RNA, membranes, and small molecules.<\/p>\n<h3>Gromacs compatible tools<\/h3>\n<h3>convertTpl\u3001ctl2mdp.pl\u3001log2form.pl<\/h3>\n<p>Creation of systems containing proteins, nucleic acids, and small molecules is easy with myPresto. myPresto converts the system files created with myPresto into input for Gromacs, a fast MD software. Gromacs output files can be converted into highly readable myPresto format files.<\/p>\n<h1><span class=\"ez-toc-section\" id=\"Structure_preparation_and_file_format_conversion_for_small_molecules_etc\"><\/span>Structure preparation and file format conversion for small molecules, etc.<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>Hgene: Hydrogen Generation ENginE<\/h3>\n<p>Addition and deletion of hydrogen atoms in dissociated and nondissociated forms at around pH 7 for small and medium organic molecules, and simple 3D structure generation. Add or remove hydrogen atoms in dissociated and non-dissociated forms, generate simple 3D structures, and add Gasteiger and MOPAC AM1BCC charges to low and medium organic molecules, MOPAC PM3 for structure optimization.<br \/>\nSupported formats are SMILES \/ ISIS MOL, SDF \/ Sybyl mol2 \/ PDB \/ mmCIF<br \/>\n<span style=\"color: #ff0000;\">Last update on March 23, 2022<\/span><\/p>\n<h1><span class=\"ez-toc-section\" id=\"Force-field_parameter_assignment\"><\/span>Force-field parameter assignment<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>tplgeneX: ToPoLogy generatinG ENginE eXtended<\/h3>\n<p>This engine is used to construct molecular topologies of biological macromolecules for use in other myPresto programs.<br \/>\nIt newly allows input\/output of atomic coordinates in PDBx\/mmCIF format and simplified handling of ligand molecule topologies.<br \/>\nSupported molecules: Proteins (including phosphorylated and methylated), nucleic acids (RNA \/ DNA), membrane molecules, water, various salts, typical solvents (DMSO, monosaccharides, etc.), metals, etc.<br \/>\nSupported force field:<br \/>\nAMBER force fields: ff99, ff99-Fuji, ff99-SB, ff99-SB-ILDN, ff99-SB-DISP<br \/>\nNucleic acid force field: ff99, ff99bsc0, OL3, YIL, ROC, Shaw<br \/>\nMembrane molecular force field: lipid14<br \/>\n<span style=\"color: #ff0000;\">Last update on March, 2022<\/span><\/p>\n<h3>tplgeneL: ToPoLogy generatinG ENginE for Ligands<\/h3>\n<p>This engine is for generating molecular topology of a target ligand (chemical compound) for usage in other programs in myPresto.<br \/>\n<span style=\"color: #ff0000;\">Last update on January 12, 2018<\/span><\/p>\n<h1><span class=\"ez-toc-section\" id=\"Membrane_system\"><\/span>Membrane system<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>membgene3<\/h3>\n<p>A tool program for modeling a system including transmembrane protein, lipid bilayer membrane, water, and ions.<br \/>\n<span style=\"color: #ff0000;\">Last updated on October 2, 2021<\/span><\/p>\n<h1><span class=\"ez-toc-section\" id=\"Free_energy_calculation\"><\/span>Free energy calculation<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>Filling potential method to calculate a binding free energy between two molecules<\/h3>\n<p>In this method, free energy profiles are obtained from the analysis of many MD trajectories which are obtained with MD calculations with umbrella potentials.<br \/>\n<span style=\"color: #ff0000;\">Last updated on March 11, 2018<\/span><\/p>\n<h1><span class=\"ez-toc-section\" id=\"Conformer_generation\"><\/span>Conformer generation<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>Confgene:Conformer Generation ENginE<\/h3>\n<p>(included in ToolsYYMMDD.tar.gz)<br \/>\nA conformer generator for compound. Confgene can generate various conformers of compound.<br \/>\n<span style=\"color: #ff0000;\">Last update on January 18, 2018<\/span><\/p>\n<h3>ConfgeneC: Conformer Generation ENginE for Cyclic part<\/h3>\n<p>(included in ToolsYYMMDD.tar.gz)<br \/>\nA conformer generator for cyclic part of compound.<br \/>\n<span style=\"color: #ff0000;\">Last update on January 18, 2018<\/span><\/p>\n<h3>descgene<\/h3>\n<p>Generate molecular descriptor files by randomly generating conformations including ring conformations and linear chains of small molecules.<br \/>\n(radius of inertia, ASA, flatness, eccentricity, MACCS key\/Joback descriptor, etc.)<\/p>\n<h1><span class=\"ez-toc-section\" id=\"Compound_database\"><\/span>Compound database<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>3DdataConstruction<\/h3>\n<p>A tool box for 3D mol2 file generation from 2D mol file. It can generate 3D compound database from a 2D chemical compound catalog.<br \/>\n<span style=\"color: #ff0000;\">Last update on December 3, 2019<br \/>\n<\/span><\/p>\n<h3><a href=\"http:\/\/www.mypresto5.com\/ligandbox\/cgi-bin\/index.cgi?LANG=en\">LigandBox: LIGANd Data Base Open and eXtensible<\/a><\/h3>\n<p>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.<br \/>\n<span style=\"color: #ff0000;\">If you want LigandBox, please specify &#8220;Your Affiliation&#8221; and apply with <a href=\"https:\/\/www.mypresto5.jp\/en\/contact\/\">Contact<\/a>. We will inform you of the download site of LigandBox by email.<\/span><\/p>\n<p>Sample of molecule files :\u00a0 <a href=\"https:\/\/www.mypresto5.jp\/en\/wp-content\/uploads\/2020\/06\/mol2.gif\">Mol2<\/a>\u00a0 <a href=\"https:\/\/www.mypresto5.jp\/en\/wp-content\/uploads\/2020\/06\/sdf.gif\">SDF<\/a><\/p>\n<h1><span class=\"ez-toc-section\" id=\"Receptor-ligand_binding_site_search\"><\/span>Receptor-ligand binding site search<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>MolSite<\/h3>\n<p>A ligand-binding site prediction. MolSite predicts ligand-binding site of target protein and its affinity by a compound docking simulation.<br \/>\n<em>Y. Fukunishi, H. Nakamura. \u201cPrediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library.\u201d Protein Science, in press.<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on January 12, 2018<\/span><\/p>\n<h3>sitegene<\/h3>\n<p>Search for concave areas on the molecular surface of proteins and nucleic acids.<\/p>\n<h3>UAP: Univeral Active Probes<\/h3>\n<p>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.<br \/>\n<em>Y. Fukunishi, K. Ono, M. Orita, H. Nakamura. \u201cSelection of in-silico drug screening result by using universal active probes (UAPs).\u201d Journal of Chemical Information and Modeling, 2010, 50, 1233-1240<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on January 19, 2018<\/span><\/p>\n<h1><span class=\"ez-toc-section\" id=\"Protein-compound_docking\"><\/span>Protein-compound docking<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>sievgene: SIEVinG ENginE<\/h3>\n<p>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 &lt; 2A in a self-docking test) on usual PC. It is designed for PC grid computing.<br \/>\n<em>Fukunishi, Y., Mikami, Y., Nakamura, H. (2005) J. Mol. Graph. Model. 24, 34-45<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on March 20, 2018<\/span><\/p>\n<h3>sievgene_M<\/h3>\n<p>sievgene_M is a modified version of sievgene, which can be also executed on a system with Intel Xeon Phi. Inte Xeon Phi is a new CPU including more than 50 cores.<br \/>\n<span style=\"color: #ff0000;\">Last update on January 20, 2018<\/span><\/p>\n<h3>sievgeneDIAV: SIEVinG ENginE with DIAV method<\/h3>\n<p>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).<br \/>\n<em>Fukunishi, Y., Nakamura, H. (2013) Pharmaceuticals 6, 604-622<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on May 7, 2022<\/span><\/p>\n<h3>sievgeneNMR: SIEVinG ENginE for NMR<\/h3>\n<p>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.<br \/>\n<em>Fukunishi, Y., Mizukoshi, Y., Takeuchi, K., Shimada, I., Takahashi, H., Nakamura, H. (2012) J. Mol. Graph. Model. 31, 20-27<\/em><br \/>\n<span style=\"color: #ff0000;\"> Last update on August 24, 2019<\/span><\/p>\n<h3>sievgeneMVO: SIEVinG ENginE for Maximum Volume Overlap<\/h3>\n<p>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.<br \/>\n<em>Fukunishi, Y., Nakamura, H. (2012) Pharmaceuticals 5, 1332-1345<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on January 11, 2018<\/span><\/p>\n<h3>Docking-score QSAR<\/h3>\n<p>Docking-score QSAR method is to predict protein\u2212compound binding energies from known activity.<br \/>\n<em>Fukunishi, Y., Yamashita, Y., Mashimo, T., Nakamura, H. (2018) Molecular Informatics 37, 1868-1743<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on February 16, 2020<\/span><\/p>\n<h1><span class=\"ez-toc-section\" id=\"in-silico_drug_screening\"><\/span>in-silico drug screening<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>selectMTS: Multiple Target Screening method<\/h3>\n<p>(included in screening_packYYMMDD.tar.gz)<br \/>\nA 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.<br \/>\n<em>Y. Fukunishi, Y. Mikami, S. Kubota, H. Nakamura, \u201cMultiple target screening method for robust and accurate in silico screening.\u201d Journal of Molecular Graphics and Modelling,25, 61-70 (2005)<\/em><br \/>\n<em>Y. Fukunishi, S. Kubota, H. Nakamura, \u201cNoise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening\u201d, Journal of Chemical Information and Modeling, 46, 2071-2084 (2006)<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on October 29, 2018<\/span><\/p>\n<h3>selectDSI: Docking Score Index method<\/h3>\n<p>(included in screening_packYYMMDD.tar.gz)<br \/>\nA 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.<br \/>\n<em>Y. Fukunishi, Y. Mikami, K. Takedomi, M. Yamanouchi, H. Shima, H. Nakamura. \u201cClassification of chemical compounds by protein-compound docking for use in designing a focused library\u201d, Journal of Medicinal Chemistry, 49, 523-533 (2006)<\/em><br \/>\n<em>Y. Fukunishi, S. Hojo, H.Nakamura, \u201cAn 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.\u201d, Journal of chemical information and modeling, 46, 2610-22 (2006)<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on January 12, 2018<\/span><\/p>\n<h3>Affinity_fingerprint: Compound database and protein-compound affinity matrix<\/h3>\n<p>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 \u201c \u201c.) 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.<\/p>\n<h3>Substrucure_search<\/h3>\n<p>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\u2019s method.<br \/>\n<span style=\"color: #ff0000;\">Last update on January 12, 2018<\/span><\/p>\n<h3>TGS: Topological Graph Search (A Similarity Search Using Molecular Topological Graphs)<\/h3>\n<p>A similarity search method based on eigen values of molecular edge matrix.<br \/>\n<em>Y. Fukunishi, H. Nakamura. \u201cA similarity search using molecular topological graphs\u201d, Journal of Biomedicine and Biotechnology, Volume 2009 (2009), Article ID 231780<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on January 13, 2018<\/span><\/p>\n<h3>MVO: Molecular-Dynamics Maximum-Volume Overlap<\/h3>\n<p>(included in ToolsYYMMDD.tar.gz)<br \/>\nA similarity search method based on overlap of molecular volume by molecular dynamics simulation.<br \/>\n<em>Y. Fukunishi, H. Nakamura, \u201cA new method for in-silico drug screening and similarity search using molecular-dynamics maximum-volume overlap (MD-MVO) method\u201d, Journal of Molecular Graphics and Modelling, 2009, 27, 628-636<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on January 18, 2018<\/span><\/p>\n<h3>MVO_screening<\/h3>\n<p>A ligand search program using the Moleclar volume overlap (MVO) method.<br \/>\n<span style=\"color: #ff0000;\">Last updated on February 27, 2018<\/span><\/p>\n<h1><span class=\"ez-toc-section\" id=\"Physical_property_estimation\"><\/span>Physical property estimation<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>Ligand property prediction<\/h3>\n<p>This is a tool for predicting physical properties of low molecular weight compounds and medium molecules using regression learning. Using learned data, predicted values of membrane permeability coefficient (LogPa, apparent permeability), distribution coefficient considering ionization (LogD, distribution coefficiene), and solubility (LogS) can be calculated.<br \/>\n<em>Y. Fukunishi, T. Mashimo, T. Kurosawa, Y. Wakabayashi, H.K. Nakamura, K. Takeuchi. \u201cPrediction of Passive Membrane Permeability by Semi\u2010Empirical Method Considering Viscous and Inertial Resistances and Different Rates of Conformational Change and Diffusion.\u201d Molecular informatics, 2019:38, 1900071<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on January 30, 2022<\/span><\/p>\n<h3>LogS_prediction<\/h3>\n<p>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.<br \/>\n<em>T. Mashimo, Y. Fukunishi, M. Orita, N. Katayama, S. Fujita, H. Nakamura. \u201cQuantitative analysis of aggregation-solubility relationship by in-silico solubility prediction.\u201d International Journal of High Throughput Screening, 2010:1, 99-107<\/em><br \/>\n<span style=\"color: #ff0000;\">Last update on January 14, 2018<\/span><\/p>\n<h1><span class=\"ez-toc-section\" id=\"Synthetic_accessibility_estimation_and_Drug_design\"><\/span>Synthetic accessibility estimation and Drug design<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>ReCGen: Generate virtual compounds based on input structure<\/h3>\n<p>This is the source code for a fragment-based virtual compound generator program.<br \/>\nThe program offers the 3 following tools: Fragment database creator tool, database merge tool, structure generator tool.<br \/>\nThe copyright for ReCGen, a compound structure generator program, is owned by Kyoto Constella Technologies Co., Ltd.<br \/>\n<span style=\"color: #ff0000;\">Last updated on March 10, 2018<\/span><\/p>\n<h3>SyntheticAccessibility: Prediction of the synthetic accessibility of given compounds.<\/h3>\n<p>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).<br \/>\n<em>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.<\/em><br \/>\n<span style=\"color: #ff0000;\">Last updated on January 11, 2018<\/span><\/p>\n<h1><span class=\"ez-toc-section\" id=\"Interface_for_new_PDB_format\"><\/span>Interface for new PDB format<span class=\"ez-toc-section-end\"><\/span><\/h1>\n<h3>LibMyPresto: Package of the library programs for parsing and writing PDBx\/mmCIF and PDB formatted files.<\/h3>\n<p>Library programs to parse and write either PDBx\/mmCIF or PDB formatted files, with the users programs in C, f77 and f90 languages.<br \/>\n<span style=\"color: #ff0000;\">Last updated on January 19, 2018<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u00a0 \u00a0 \u00a0 \u00a0User Manual v5.000 Simple software package with graphic interface myPresto Portal myPresto Protal is a graphic user interface (GUI) program for myPresto and GROMACS, available for Windows, MAC and Linux (all 64bit). Last updated on February 4, 2026 myPresto Portal Quick Manual Easy myPresto Easy myPresto is a graphic user interface (GUI) program for myPresto, available for Windows, MAC and Linux (all 64bit). Last updated on January 11, 2024 Easy myPresto Manual (Japanese) The free version is distributed through the generosity of member companies, with restrictions on molecular weight, functions, etc., to paid software. MolDesk EC shop Paid version of Easy myPresto Molecular dynamics simulation cosgene: COnformation&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"tags":[6,10,8,5,7,9],"_links":{"self":[{"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/pages\/15"}],"collection":[{"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/comments?post=15"}],"version-history":[{"count":150,"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/pages\/15\/revisions"}],"predecessor-version":[{"id":1691,"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/pages\/15\/revisions\/1691"}],"wp:attachment":[{"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/media?parent=15"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.mypresto5.jp\/en\/wp-json\/wp\/v2\/tags?post=15"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}