Institute of Molecular Function








   Last Modified

   8 February 2019

Theoretical Organic Chemistry Nuclear Receptor Chemistry Structural Bioinformatics Rational Drug Design

Homology Modeling for HyperChem Logo Gaussian Interface for HyperChem Logo Full-Auto Interactive, Muti-layer ONIOM Interface Logo Docking Study with HyperChem Logo Mol Dimension Logo Virtual Screening System Technology AutoDock Vina In Silico Screenings Interface The Next-generation Drug Design Technology Drug Design Methodology for Organic Chemists MFDD In Silico Drug Design Research Service HyperChem


Docking Study with HyperChem

Essential, Premium Essential, Professional, Advanced, Ultimate, and Cluster


What's New in Revision F1.


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.


Control Center, Black ColorControl Center, Windows Default Color

Control Center, Dark ColorDocking Study Module

Dock Viewer ModuleMol Dimension Module

Mol Browser ModulePIEFII Module, Setup Mode

PIEFII Module, Pharmacophore Predictions


The following shows the addition functions to the previous revision.

Improvement for Windows 7 and Vista (32 bit or 64 bit (WOW64) version) environments

Correspondence to the latest HyperChem version

Improvement of the clustering functions (only Cluster version)

Improvement of functions


Manual Contents (Japanese Language)


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



Homology Modeling for HyperChem


What's New in Revision F1.


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.


Control Center, Windows ColorEstimation of Hydrogen Atoms in Water Module

Homology Modeling ModuleInteface Selection Module

Peripheral Modeling ModuleProtein Superposition Module

Restraints ModuleSide-chain Rotamer Modeling Module

Ramachandran Plot ModuleTrajectory Analyzer Module

Gaussian Interface ModuleONIOM Interface Module


The following shows the addition functions to the previous revision.

Improvement for Windows 7 and Vista (32 bit or 64 bit (WOW64) version) environments

Correspondence to Gaussian09W (Single- or Multi-Processor version)

Correspondence to the latest HyperChem version

Improvement of functions


Added the Homology Search and Homology Modeling Reference manual.

Reference Manual Contents (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 E1 and E2 2008/10

What's New in Revision D1 2008/05

What's New in Revision C2. 2007/11

What's New in Revision C1. 2007/02



Site Map 

Copyright (C) 2004-2019 Institute of Molecular Function. All Rights Reserved.