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Attachment 2 The requirements listed in the table below shall be accommodated by the responder offering a Drug Discovery Software Platform. Please indicate Y (Yes) or N (No) if your product meets each requirement in the requirements list below, and use the comments column to further justify how your product meets the requirement.
REQUIREMENTS/ SPECIFICATIONS
Meets Requirement?
(Y/N) Comments
The Drug Discovery Software Platform shall meet the following requirements:
| 1 |
| Model drug-protein interactions and other small molecule interactions with enzymes for biomedical research. |
| 2 |
| Detect and visualize active sites, diagram ligand binding, draw electrostatic interaction maps, generate 3D models of ligands, incorporates bioinformatics and cheminformatics analysis. |
| 3 |
| Perform partial matches based on patterns, pharmacophores, constraints, and shapes. |
| 4 |
| Generate automatic queries and create conformational databases. |
| 5 |
| Provide molecular modeling and simulations capabilities which allows quantum and semi-empirical calculations and predictions of molecular surfaces and electron density display. |
| 6 |
| Integrated single package for protein design tools, homology modeling, small-molecules 2D and 3D structures and store them into a table, in-silico screening of large chemical database, QSAR and Molecular Dynamics. |
| 7 |
| Function without an internet connection but allows access to the internet in order to search scientific databases containing DNA sequence samples and other depersonalized data. |
| 8 |
| Handle large biological molecules and use several different force fields for molecular simulations and several different scoring functions for in-silico screening. |
| 9 |
| Setup input files for MM2 molecular mechanisms and MOPAC molecular orbital calculations other advanced quantum chemistry software. |
| 10 |
| Run and produce the same results under various operating systems, such as Windows 10, Macintosh and Unix/Linux operating systems. |
| 11 |
| Easy to learn and work with scripting language and availability of large number of scripts to do new set of calculations. Additional scripts for future projects should be available within a month or so without waiting for the newer update of the software. |
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