REVISED SpecDoc.docx

Statement of Requirements Annual in silico protein modeling software licenses

GENERAL INFORMATION

The USDA, ARS has a requirement for a comprehensive bioinformatics, cheminformatics, molecular modeling, and computational chemistry suite. The requirement will be met by a single all-in-one in silico protein modeling software for allergen characterization, to define structural and chemical characteristics of peanut and tree nut allergens, evaluate allergen peptide simulations, visualize and portray allergen modifications, define molecular antibody-allergen interactions, and characterization of processing effects on food allergens.

This requirement is for single platform protein modeling software capable of deterministic structure prediction, protein-protein docking determinations, and molecular simulation for small molecule and protein structure perturbations due to structural and chemical modification due to food processing treatments. The software will be used to exceed the capabilities of generally available bioinformatics software including, but not limited to: PubMed, NCBI BLAST, RCSB/PDB, Clustal Omega, and Chimera commonly utilized for base level experimental procedures related to protein, antibody, and allergen interaction modeling. In silico modeling results will be used to guide development of improved processing steps, antibody development, and mutations resulting in allergen attenuation. The in silico allergen and antibody modeling and docking with the Molecular Operating Environment (MOE) software will be used to characterize important protein-protein contacts essential for allergen-antibody interaction. MOE is recognized as the only commercially available software package that provides all necessary modeling capabilities for generating multiple variant model types from a single dataset, facilitating cohesive project management and scientific documentation.

The software will be used for the base year and four potential optional years.

Technical Requirements, minimum specifications and essential characteristics

· Single interface (not multi-modular) software application for in silico protein modeling

· Licensing for at least one year of software access and support

· Complete training for software use and updates

· Ensure software compatibility with existing USDA software, virus protection, computer safety and operating systems

Minimum specifications

· Annual software license including one-on-one support and updates

· Advanced Scripting Language (SVL) for developing custom modeling techniques

· A repository of community-generated SVL scripts accessible to users

· Floating licenses allowing multiple scientists to use the software across various systems

· Active site visualization

· Protein Ligand Interaction Fingerprints and epitope prediction

· Protein surface patch prediction

· Amino acid customization and chemical modification

· Ligand modification/optimization

· Virtual library enumeration

· Descriptor calculations

· Small molecule alignments, solvent and conformational analysis

· Protein, allergen, and antibody modeling

· Antibody library inclusive and updated annually

· Disulfide and alanine scanning for mutational analysis

· Protein-protein and protein-peptide docking

· Molecular simulations and quantum calculations

Essential Characteristics required:

· Shall be capable of storing structure-based databases and their associated toxicity information

· Shall be capable of extracting correlations based on molecular descriptors

· Shall be capable of identifying off-target interactions and predicting interactions

· Shall exist in an internally installed client-server version that can access user stored proprietary data

· Shall allow the user to create, edit, save and share results obtained from the platform

· Shall have the ability to conduct chemical searches

· Shall be capable of exporting results and compatible with commonly used data management and visualization tools

· Shall be eligible for regular updates and support

· Shall be customizable and programmable

· Shall be capable of identifying protein-ligand interactions

· Shall be capable of protein/peptide modeling and simulations

· Shall be capable of performing clustering analysis