Last Modified
1 January 2024
Products
Collaborative Research (MFDD In Silico Drug Design Research Service)
Commissioned Calculation Service
Molecular Modeling and Structure-based Drug Design Systems
Structure-based Drug Design System Flow Chart
| Target Disease (Target Gene) | Structure-based Drug Design System | |||
| ↓ | ↓ | |||
| Target Amino-acid Sequence | → | Protein Homology Modeling | → | Homology Modeling for HyperChem |
| ↓ | Structural Refinement of Biomacromolecular System | Gaussian Interface for HyperChem | ||
| ↓ | ↓ | |||
| Target Structure of Biomacromolecular System | → | in silico Screening | → | AutoDock Vina Screenings Interface |
| ↓ | Preparation of Compound Library | Docking Study with HyperChem | ||
| ↓ | Ligand Binding Site Prediction | Virtual Screening System | ||
| ↓ | ↓ | |||
| Biomacromolecule - Ligand Complex | → | Analysis of Complex | → | Docking Study with HyperChem |
| ↓ | Precise Docking Simulations | ONIOM Interface for Receptor | ||
| ↓ | Gaussian Interface for HyperChem | |||
| ↓ | ↓ | |||
| Lead Compound | → | Lead Optimizations | → | AutoDock Vina Screenings Interface |
| ↓ | Docking Study with HyperChem | |||
| ↓ | Virtual Screening System | |||
| Drug Candidate |
Products
Package Module Programs |
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| Revision H1 | Revision H1 | ||
| Professional | Max. 1 Compound ~ Unlimited | ||
| Control Center |  |
ü | ü |
| Estimation of Hydrogen Atoms in Water |  |
ü | |
| Geometry Correction |  |
ü | ü |
|
Homology Modeling (Professional)
|
 |
ü | |
| Interface Selection |  |
ü | ü |
| Peripheral Modeling (Professional)
|
 |
ü | |
| ONIOM Interface |  |
ü | |
| Gaussian Interface |  |
ü | |
| Protein Superposition |  |
ü | |
| Ramachandran Plot |  |
ü | |
| Restraints |  |
ü | |
| Side Chain Rotamer Modeling (Professional)
|
 |
ü | |
| Trajectory Analyzer |  |
ü | |
| Docking Study |  |
ü
Single ~ Unlimited |
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| Dock Viewer |  |
ü Unlimited |
|
| Mol Browser |  |
ü Unlimited |
|
| Mol Dimension |  |
ü Single ~ Unlimited |
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| PIEFF |  |
ü Simultaneous Predictable Atoms 1000 (ca. 80 Residues) ~ Unlimited |
|
| AutoDock Vina In Silico Screenings Interface | ü Unlimited |
||
| Homology Modeling Professional for HyperChem Manual (Japanese) |
ü | ||
| Homology Modeling Professional for HyperChem Manual 2 (Japanese) |
ü | ||
| Homology Modeling Professional for HyperChem Referece (Japanese) |
ü | ||
| Docking Study with HyperChem Manual (Japanese) |
ü | ||
| Docking Study with HyperChem Manual 2 (Japanese) |
ü | ||
Docking Study with HyperChem Family
Family Module Programs |
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| Essential | Premium Essential | Professional | Advanced | Ultimate | Cluster | ||
| Control Center |  |
Non-limited | Non-limited | Non-limited | Non-limited | Non-limited | Non-limited |
| Geometry Correction | |
Non-limited | Non-limited | Non-limited | Non-limited | Non-limited | Non-limited |
| Docking Study | |
Single Compound | Max. 10 Compounds | Max. 100 Compounds | Max. 1,000 Compounds | Max. 10,000 Compounds | Non-limited, Cluster |
| Dock Viewer | |
Non-limited | Non-limited | Non-limited | Non-limited | Non-limited | Non-limited |
| Mol Browser | |
Non-limited | Non-limited | Non-limited | Non-limited | Non-limited | Non-limited |
| Mol Dimension | |
Single Compound | Max. 10 Compounds | Max. 100 Compounds | Max. 1,000 Compounds | Max. 10,000 Compounds | Non-limited, Cluster |
| PIEFII | |
Limited Version | Limited Version | Limited Version | Limited Version | Limited Version | Non-limited Version |
|
AutoDock Vina Screenings |
Non-limited | Non-limited | Non-limited | Non-limited | Non-limited | Non-limited | |
Software Requirement*,**
| Software | Producer | Feature | Related Site |
| HyperChem for Windows |  |
The Most Powerful Molecular Modeling Environment | HyperChem Outline |
| Gaussian for Windows |  |
The Most Powerful Computational Chemistry Environment | |
| TclPro1.2 for Windows |
  |
HyperChem Developer's Environment | Download Site (Free) |
* HyperChem is a registered trademark of Hypercube, Inc.
** Gaussian is a registered trademark of Gaussian, Inc.
Others
| Title | Comments |
| Homology Modeling Reference for HyperChem | old product: Homology Modeling for HyperChem, Revision A2, Reference Manual |
Collaborative Research (MFDD In Silico Drug Design Research Service)
| Available Techniques (examples) |
| Homology Modeling (Protein, Protein-Ligand Complex, Protein-Protein Complex, Protein-Nucleic Acid Complex, etc.) |
| Protein Secondary Structure Prediction |
| 3D Structure Prediction |
| Molecular Dynamics Simulations |
| Ligand Binding Site Prediction |
| Docking Study (Biomacromolecule-Compound, Biomacromolecule-Biomacromolecule, Biomacromolecule-Peptide, etc.) |
| Biomacromolecular System Modeling (Molecular Systems consisted of Proteins, Nucleic Acids, Compounds, Metal Atoms and Waters) |
| in silico Screening (Structure-based, etc.) |
| Compound Database and Library Preparations |
| Drug Design, Lead Optimizations |
| Ligand-based Screenings |
| Molecular Modeling |
| Quantum Mechanics Calculations |
| QM/MM Calculations |
| Others |
* There are many experiences for 15 years.
Commissioned Calculation Service
Calculation agency service for small and medium compounds with approximately 1,000 molecular weight (Molecular Mechanics, Molecular Dynamics, Semi-empirical Molecular Orbital Methods, Hartree-Fock Theory, Meller-Plesset Pertubation Theory, Density Functional Theory).
| Available Techniques (examples) |
| Structural Optimizations |
| Molecular Dynamics |
| Conformational Search |
| Molecular Orbital Methods (HOMO and LUMO levels) |
| Excite State Analysis (Singlet and Triplet States) |
| Dipole Moment |
| NMR Chemical Shift Predictions |
| IR Chart Predictions |
| UV Chart Predictions |
| Solvent Effect Calculations |
| LogP Predictions |
| Illustration |
| Others |