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Last Modified 23 February 2018 |
Announce The Latest In Silico Drug Design Platform: Evolution of Docking Study with HyperChem, Revision H1 and Homology Modeling Professional for HyperChem, Revision H1. Strengthened quantum mechanics calculation program, Gaussian,ONIOM Interface, compatible to file format of molecular dynamics calculation program, NAMD (VMD: CHARMM-based PDB), compatible to file format of fragment molecular orbital calculation programs, ABINIT-MP (BioStation Viewer) and GAMESS (Fu /Facio), and supported AutoDock Vina Virtual Screening Interface (preparation of compound database - preparation of all input files - execution - viewing and filtering of hits; supports also simultaneous analysis of both Docking Study and AutoDock Vina results)
In quantum mechanics calculations for the entire structure of big molecular system such as biomacromolecular system, the single point calculations for the initial structure obtained from classical molecular mechanics calculations and/or classical molecular dynamics calculations cannot converge or will give abnormal energies. For obtaining reliable results from quantum mechanics calculations such as fragment molecular orbital methods of entire molecular system, the initial structure must be prepared using geometrical optimization calculations via ONIOM methods. ONIOM Interface for Receptor can provide the best solution for the quantum mechanics calculations of the entire molecular system of which the precise initial structure is prepared from Docking Study with HyperChem and Homology Modeling Professional for HyperChem. Motonori Tsuji, et. al. FEBS Open Bio., 7, 391-396, 2017, DOI: 10.1002/2211-5463.12188.
Docking Study with HyperChem, Revision H1 with AutoDock Vina In Silico Screenings Interface Compatible to NAMD Molecular Dynamics and ABINIT-MP / GAMESS Fragment Molecular Orbital Quantum Mechanics Calculations for Entire Molecular System - Carrying The Next-generation Drug Discovery Technology, The PIEFII Technology -
Powered by Docking Study with HyperChem THE IMPOSSIBLE BECOMES POSSIBLE. Advanced Technology & The High-Performance, Biomacromolecule- & Ligand-Flexible Docking & Screening Program Package Docking Study with HyperChem supports the comprehensive and automatic biomacromolecule (protein and nucleic acid molecule systems)- and ligand (small molecule and peptide)-flexible docking simulations, and thus supports the drug design and the in silico screening of a drug candidate.
Homology Modeling Professional for HyperChem, Revision H1 with Gaussian Interface for HyperChem & ONIOM Interface for Receptor Compatible to NAMD Molecular Dynamics and ABINIT-MP / GAMESS Fragment Molecular Orbital Quantum Mechanics Calculations for Entire Molecular System
Powered by Homology Modeling Professional for HyperChem THE IMPOSSIBLE BECOMES POSSIBLE. New, High-Performance Software for Biomacromolecular System Modeling, Functional Analysis, and Simulation. Homology Modeling Professional for HyperChem is the latest molecular modeling package which can carry out the molecular modeling, functional analysis, and simulations of a big molecular system using comprehensively the ab-initio quantum chemistry calculations and the molecular dynamics simulations as well as the molecular mechanics calculations. The program can control seamlessly both HyperChem and Gaussian packages and can be simultaneously fed back their calculation results to the big molecular system in the HyperChem graphical user interface. The whole molecular system can be operated in a quantum chemistry via the full-automatic ONIOM interface to Gaussian. All operations are fully automated in the GUI-based manner, and thus the program supports the logical molecular modeling, functional analysis, and simulations in the life science research such as the structure-based drug design, as well as an unexplored research.
The Next-generation Drug Discovery Technology Ab-Initio Biomacromolecule-Ligand Interaction Site Structure-based Pharmacophore Prediction Technology Potential Ligand Prediction Technology
Latest News Archives 2018/03/27 Motonori Tsuji will speak a research entitled "Antagonist-Perturbation Mechanism for Activation Function-2 Fixed Motifs: Active Conformation and Docking Mode of Retinoid X Receptor Antagonists" at the 138th annual meeting of the pharmaceutical society of Japan. 2018/02/23 Announcing Docking Study with HyperChem, Revision H1 and Homology Modeling Professional for HyperChem, Revision H1. 2018/01/09 The Latest In Silico Drug Design Platform: Evolution of Docking Study with HyperChem, Revision H1 and Homology Modeling Professional for HyperChem, Revision H1. Coming Soon. (Strengthened quantum mechanics calculation program, Gaussian, ONIOM Interface, compatible to file format of molecular dynamics calculation program, NAMD (VMD: CHARMM-based PDB), compatible to file format of fragment molecular orbital calculation programs, ABINIT-MP (BioStation Viewer) and GAMESS (Fu /Facio), and supported AutoDock Vina Virtual Screening Interface (preparation of compound database - preparation of all input files - execution - viewing and filtering of hits; supports also simultaneous analysis of both Docking Study and AutoDock Vina results)) 2017/11/19 Motonori Tsuji spoke a research entitled "Identifying the Receptor Subtype Selectivity of Retinoids via Docking, QM/MM, and Quantum Mechanics Calculations: ATRA Can Act as an Endogenous RXR Ligand" at the 28th symposium of retinoids of Japan society for retinoid research. 2017/05/16 Origin of the agonism and antagonism mechanisms in the nuclear receptors via quantum mechanics (using core technologies of Docking Study with HyperChem and Homology Modeling Professional for HyperChem) has been accepted for publication. Motonori Tsuji. J. Comput. Aided Mol. Des. 31, 577-585, 2017, DOI: 10.1007/s10822-017-0025-6. 2017/04/16 Confirmed that the products are compatible to Gaussian16W 64-bit multi-processor version (Revision A.03). I really appreciate great help of Gaussian, Inc. 2017/03/28 All series of HyperChem of Hypercube, Inc. are available from our web site. 2017/03/27 Motonori Tsuji spoke a research entitled "Helix H3 Three-Point Initial-Binding Hypothesis: Understanding of Both the Ligand-Trapping Mechanism and the Simultaneous Structural Transition from Apo-Form to Holo-Form of the Ligand-Binding Domain in the Nuclear Receptor Superfamily" at the 137th annual meeting of the pharmaceutical society of Japan. 2017/02/15 Press Release: Origin of the receptor subtype selectivity via quantum mechanics has been published. Motonori Tsuji, et. al. FEBS Open Bio. 7, 391-396, 2017, DOI: 10.1002/2211-5463.12188. 2016/12/29 Origin of the receptor subtype selectivity via quantum mechanics has been accepted for publication. 2016/04/16 Confirmed that ONIOM Interface for Receptor and Gaussian Interface for HyperChem were compatible with the latest Gaussian09W (64bit-multiprocessor version, Revision E.01) under support of Gaussian, Inc. I really appreciate great help of Gaussian, Inc. 2016/03/27 Motonori Tsuji spoke a research entitled "Geometrical Dependence of the Highest Occupied Molecular Orbital in Bicyclic Systems: Origin of the Facial Stereoselectivity of Bicyclic Olefins" at the 136th annual meeting of the pharmaceutical society of Japan. 2016/03/26 Announcing Docking Study with HyperChem 2016 and Homology Modeling Professional for HyperChem 2016, Revision G1. 2016/03/26 The function of ONIOM Interface for Receptor was strengthened (compatible to whole system of protein and nucleic acid molecular system). 2015/12/01 Confirmed that Docking Study with HyperChem and Homology Modeling Professional for HyperChem were compatible with Windows 10 Professional (64 bit Version). 2015/11/04 Press Release: Origin of the ligand recognition mechanism in the nuclear receptor superfamily has been published. Motonori Tsuji. J. Mol. Graph. Model. 62, 262-275, 2015. 2015/10/07 The first success of the structural transition of the holo-form formation simulations and the discovery of the driving forces involved in the ligand entry in the nuclear receptor superfamily using Docking Study with HyperChem and Homology Modeling Professional for HyperChem has been accepted for publication. 2015/09/13 A proposed molecular mechanism of ATRA via retinoid X receptors (using core technologies of Docking Study with HyperChem and Homology Modeling Professional for HyperChem) has been accepted for publication. Motonori Tsuji, et. al. J. Comput. Aided Mol. Des. 29, 975-988, 2015. 2015/04/17 Press Release: Origin of the facial stereoselectivity, which is the most important and unsolved issue in organic chemistry, has recently been accepted for publication. Motonori Tsuji. Asian J. Org. Chem. 4, 659-673, 2015. 2015/03/26 Motonori Tsuji spoke a research entitled "Structure and function of the local motifs in the canonical structure of the ligand-binding domain in the nuclear receptor superfamily" at the 135th annual meeting of the pharmaceutical society of Japan. 2015/01/04 Announcing Docking Study with HyperChem 2015 and Homology Modeling Professional for HyperChem 2015, Revision G1. 2014/10/14 Announcing Docking Study with HyperChem and Homology Modeling Professional for HyperChem, Revision F3. 2014/10/02 Confirmed that Docking Study with HyperChem and Homology Modeling Professional for HyperChem were compatible with Windows 10 Technical Preview (64 bit Version). 2014/03/18 A paper regarding the folding mechanism and the agonism and atagonism mechanism of the ligand-binding domain in the nuclear receptor superfamily has recently been published. Motonori Tsuji J. Struct. Biol. 185, 355-365, 2014.
Topics 2017/05/16 Origin of the agonism and antagonism mechanisms in the nuclear receptors via quantum mechanics has been accepted for publication. Motonori Tsuji. J. Comput. Aided Mol. Des. 31, 577-585, 2017, in press, DOI: 10.1007/s10822-017-0025-6. 2017/04/16 Confirmed that the products are compatible to Gaussian16W 64-bit multi-processor version (Revision A.03). I really appreciate great help of Gaussian, Inc. 2017/03/28 All series of HyperChem of Hypercube, Inc. are available from our web site. 2016/12/29 Origin of the receptor subtype selectivity via quantum mechanics has been accepted for publication. Motonori Tsuji, et. al., FEBS Open Bio. 7, 391-396, 2017, DOI: 10.1002/2211-5463.12188. 2016/04/16 Confirmed that the products are compatible to Gaussian09W 64-bit multi-processor version (Revision E.01). I really appreciate great help of Gaussian, Inc. 2015/10/07 Origin of the ligand recognition mechanism in the nuclear receptor superfamily has been published. Motonori Tsuji. J. Mol. Graph. Model. 62, 262-275, 2015.
2015/09/13 A proposed molecular mechanism of ATRA via retinoid X receptor (using core technologies of Docking Study with HyperChem and Homology Modeling Professional for HyperChem) has been accepted for publication. Motonori Tsuji, et. al. J. Comput. Aided Mol. Des. 29, 975-988, 2015. 2015/04/17 Discovery of the underlying rule for the facial stereoselectivity, which is the most important and unsolved issue in organic chemistry, has recently been accepted for publication. Motonori Tsuji. Asian J. Org. Chem. 4, 659-673, 2015.
2014/03/18 A paper regarding the folding mechanism and the agonism and atagonism mechanism of the ligand-binding domain in the nuclear receptor superfamily has recently been published. Motonori Tsuji. J. Struct. Biol. 185, 355-365, 2014.
2013/07/01 10th Anniversary 2012/11/30 Acquired patent rights regarding structural-based pharmacophre prediction technology. 2012/07 Homology Modeling Professional for HyperChem was cited in an article.Plant Cell Physiol. 2012 Jul; 53 (9): 1638-1647. 2010/12 Homology Modeling Professional for HyperChem was cited in an article.Biochemistry 2010 Dec; 49 (50): 10647-10655. 2010/04/30 Homology Modeling Professional for HyperChem was cited in an article.Biochemical and Biophysical Research Communications 2010 Apr 30; 339 (2): 173-177. 2008/02 Docking Study with HyperChem and Homology Modeling Professional for HyperChem were cited in an article. Science 2008 Feb 1; 319 (5863): 624-7. 2008/01/11 Motonori Tsuji was invited as a guest speaker at Business Research Institute. 2007/11/15 HyperChem of Hypercube, Inc. is available as bundle with my products. 2007/06/29 Docking Study with HyperChem and Homology Modeling Professional for HyperChem were introduced in an article. Motonori Tsuji. Molecular Science 2007; 1: NP004. 2007/06/16 I really appreciate great cooperation of Neil S. Ostlund, President and Chief Executive Officer of Hypercube, Inc. 2006/06/05 Docking Study with HyperChem is available. 2005/12/01 Homology Modeling Professional for HyperChem is available. 2005/11/28 Gaussian Interface for HyperChem and ONIOM Interface for Receptor are available. 2005/08/09 My products have been linked to the Gaussian Official site. 2005/07/11 Homology Modeling for HyperChem is available. 2005/05/01 Institute of Molecular Function Web site is started. 2003/08/06 A paper regarding the electronic structure of carboranes and the most stable conformation of cyclopropane ring has been accepted for publication. J. Org. Chem. 69, 4063-4074, 2004. 2003/08/06 A paper regarding carboranyl carbocation has been accepted for publication. J. Org. Chem. 68, 9589-9597, 2003. 2003/07/01 Institute of Molecular Function has been established by Motonori Tsuji.
* HyperChem is a registered trademark of Hypercube, Inc. *" Gaussian is a registered trademark of Gaussian, Inc.
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