In the News..

28-09-2006

HyperChem for Mac

HyperChem for Mac B.1 is designed for the PowerPC processor that Apple traditionally used. The supported machines include Mac mini, iMac, iBook, PowerBook, and PowerMac. Unfortunately the G5 machine is not supported due to the fact HyperChem is 32-bit and is not compatible with the 64-bit G5.

HyperChem for Mac B.2 for the newest release from Apple of the Intel Mac.

Docking Module for HyperChem

Advanced Technology

Since the energy calculations do not use the grid algorithm, the program does not underestimate a critical interaction energy arising from a potential energy that is sharply lowered, thus giving a highly-precise structure of a stable complex between the protein and the compound. There are no limitations to kinds of protein molecule system, since the program does not use a probe atom by which the ligand-binding site of the target protein is pre-treated in order to simplify energy calculations in the grid algorithm.

The program supports many force field calculations, i.e., MM+, Ambers, Amber2, Amber3, Amber94, Amber96, Amber99, OPLS, BIO+83, BIO+85, CHARMM19, CHARMM22, and CHARMM27 under the United Atom and All Atom conditions. Both the United Atom and the All Atom conditions can be applied to the desired parts of the protein and compound structures individually and simultaneously. These force field calculations can carry out under many minimization algorithm (Steepest Descent, Flether-Reeves, Polak- Ribiere, Newton-Raphson) supported by HyperChem, as well.

The program can assign the atomic charges of a trial compound at each conformation using the single-point calculations of a certain semi-empirical molecular orbital method. Thus, the program can perform the latest docking simulations using the atomic charges altered by the structural changes.

When the program is combined to the Gaussian Interface and ONIOM Interface of Homology Modeling for HyperChem, the program can provide the latest technology such as the QM:MM like docking simulations and the precise analysis of the obtained complex using the high-level ab initio quantum chemistry calculations such as a bond generation, a transition state analysis, and an excited state analysis.

The protein flexibility can apply to the desired parts such as some residues in the ligand-binding site, hydrogen atoms, and entire structure. In addition, the flexibility of the protein molecule system can apply to any molecules such as water molecules, small molecules, and other biological molecules. This flexibility setting is completed by selecting a part of structure using selection tool provided in the package just before simulating.

The protein system can contain any type of molecules such as metal, metal complex, small molecule, nucleic acid, and other biological molecules. The program can simulate the docking of compound, even though the ligand-binding site lies on several protein molecules.

The program can freely modify the interaction energy equation to reproduce the structure-activity relationship via the multiple linear regression analysis.

The program supports the restart function which can restart or start the docking simulations from a desired conformation without loss of the calculation precisions. The batch calculation of the docking simulations is also available when this function is used. Thus, the function is useful for searching precisely the best docking mode of the very flexible compound that has ten or more torsional bonds.

Although the program carries an algorithm optimized to the docking simulations, many high-speed techniques developed for the virtual screenings such as the loose conformation search and conformational stability test techniques are also available.

Moreover, these advanced technologies are based on our PIEFII technology which can precisely predict the protein-ligand interaction site and the potential ligand pharmacophore and scaffold.