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   Last Modified

   3 July 2017

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Docking Study with HyperChem

Essential, Premium Essential, Professional, Advanced, and Ultimate

 

What's New in Revision E1, E2.

 

The full-automatic and comprehensive biological macromolecule (protein and nucleic acid molecule systems)- and ligand (small molecule and peptide)-flexible docking simulations and in silico screenings program.

It's easy to treat the comprehensive conformation search of compound, induced fit effects of the side chain and main chain of the biological macromolecule, and the flexibility of the other molecules such as water molecules, biological molecules, small molecules, and metal atoms, etc.

The program (non-grid algorithm) can predict the precise interaction energy for the entire system rather than the approximated interaction energy obtained from the other docking simulation programs which adopt the grid algorithm for simplifying the energy calculations.

The program adopts the high reliable search method of stable complex using our novel docking algorithm based on the PIEFII technology which can precisely predict the binding site and ligand pharmacophore points in terms of the structure based manner.

In addition to general functions required for the docking simulations and screenings, the flexible docking function in consideration of the induced fit effect of biological macromolecules, the flexible docking function in consideration of large structural changes such as transformation between apo and holo conformations, the flexible docking function under the steric and electronic influences from any other molecules such as the macromolecules, small molecules, water molecules, metal atoms, and substituent groups bound to the target molecule, the atomic charge reassignment function for each conformations using any semi-empirical molecular orbital methods, any combinations of the united atom and all atom conditions, the restart function, the docking function under the solvated conditions, clustering function can be used for performing the precise docking simulations and in silico screenings. Moreover, power users can freely alter any parameters for the docking simulations and screenings as well as those for the molecular mechanics and quantum mechanics calculations via the provided graphical user interfaces.

The high-performance protein-protein, protein-nucleic acid, and nucleic acid-nucleic acid docking algorithm has been carried on the program, although this function is not available in Revision E1 (maybe available in the next revision).

 

 

The following shows the addition functions to the previous revision.

Sophisticated many functions carried on Revision D1.

Renewed the user interface of all module programs.

Window color can be selected among the Windows default color, Dark color, and Black color.

Confirmed stable performance for the molecular system exceeding 100,000 atoms (up to 65,000 atoms for single point and optimization calculation in HyperChem7.52 or later).

Transferred to the multiple window system from the modal window system.

Added the window management function.

Provided more sophisticated docking simulation and in silico screening environment to the Control Center module program.

Revised the User's manual (Japanese language).

Manual Contents (Japanese Language)

 

Docking Study with HyperChem (PDF: 2 MB; Japanese)

 

 

Homology Modeling for HyperChem

 

What's New in Revision E1, E2.

 

Homology Modeling 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 package can be used for performing the protein homology modeling in the presence or absence of the small molecules, water molecules, other biological molecules, metal atoms, and the small molecule covalently bound to the model under the vacuum or the various solvated conditions. The package also provides the several modeling, simulating, and analyzing functions.

 

 

The following shows the addition functions to the previous revision.

Sophisticated many functions carried on Revision C2.

Renewed the user interface of all module programs.

Window color can be selected from both the Windows default color and Dark color.

Confirmed stable performance for the molecular system exceeding 100,000 atoms (up to 65,000 atoms for single point and optimization calculation in HyperChem7.52 or later).

Transferred to the multiple window system from the modal window system.

Added the window management function.

Transferred the common mathematical functions to the C++ dynamic link library (the program uses the HyperChem back-ended computational engines).

Provided the homology search environment to the Control Center module program.

Added the Homology Search and Homology Modeling Reference manual.

Reference Manual Contents (Japanese Language)

Revised the User's manual (Japanese language).

Manual Contents (Japanese Language)

 

Homology Modeling Professional for HyperChem (PDF: 4 MB; Japanese)

 

SBDD Pamphlet (PDF: 2 MB; Japanese)

 

For early revisions:

What's New in Revision D1

What's New in Revision C2.

What's New in Revision C1.

 

 

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