SOLICITATION NOTICE
D -- Molecular Modeling and Chemoinformatics Programming Toolkits
- Notice Date
- 7/28/2004
- Notice Type
- Solicitation Notice
- NAICS
- 541519
— Other Computer Related Services
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD, 20894
- ZIP Code
- 20894
- Solicitation Number
- RFQ-04-195-KDR
- Response Due
- 8/11/2004
- Archive Date
- 8/26/2004
- Point of Contact
- Karen Riggs, Contracting Officer, Phone 301 496-6546, Fax 301 402-0642, - Cara Calimano, Office Automation Assistance, Phone 301 496-6127, Fax 301 402-8169,
- E-Mail Address
-
kr33v@nih.gov, CalimaC@mail.nlm.nih.gov
- Description
- This is a synopsis being conducted under Simplified Acquisition Procedures in accordance with FAR Part 12. This solicitation document incorporates provisions and clauses that are in effect through the September 2001 Federal Acquisition Regulation revision, which includes the consolidation of all Federal Acquisition Circulars through 97-27. It is the intent of the National Library of Medicine (NLM) to purchase a comprehensive suite of molecular modeling and chemoinformatics programming toolkits. It is the intention of the NLM to purchase a comprehensive suite of molecular modeling and chemoinformatics programming toolkits with the following characteristics: 1) Robust chemoinformatics and molecular data handling including: maximum common substructure and exact substructure searching, perception of aromaticity with multiple models, ring perception and Kekule-form normalization, tetrahedral and E/Z stereochemistry recognition, molecular normalization and canonicalization, support for residues and bases, multiconformer molecule handling, ability to store and recall generic primitives or user-defined objects on molecules, atoms, bonds, or conformers, and robust reading and specification-compliant writing of SMILE, SLN, SDF, MOL, MOL2, PDB, FASTA, MOPAC, MacroModel, XYZ, and OEBinary file formats; 2) State-of-the-art naming and structure rendering of compounds including: generation of structure diagrams (2D coordinates) from names, SMILES or 3D coordinates, rendering or images (GIF, BMP, EPS) of structure diagrams, naming (IUPAC) of chemical structures or connection tables; 3) Small molecule and protein charge states including: pKa state enumeration, tautomer enumeration and canonicalization, partial charges using MMFF and AM1?BCC methods, protein pKa and protein charge assignment, electrostatic descriptors and electrostatics map storage; 4) Systematic high-throughput conformer generation, including: 3D structure generation from connection tables, conformational ensemble generation with user?configurable resolution, and compact storage of multi-conformer data structures; 5) Fast structure refinement of ligands in gas-phase, in solution with more than one salvation model, or within a protein active site using MMFF force fields and capable of minimization in several coordinate frames and with constrained coordinates; 6) Molecular shape comparisons based on rapid 3D structure overlays including: molecular descriptors for shape (steric multipoles), evaluation and optimization of volume overlap between molecules and spatial similarity of chemical groups, sufficient of diversity analysis of libraries consensus shape generation, N*N shape clustering, generation of binary shape fingerprints, shape factoring in activity analysis, partial shape matching (Tversky measure) , and D-optimal design on conformationally expanded libraries; and 7) Efficient solution of Poisson-Boltzmann electrostatics in a medium of varying dielectric, including multi-grid methods and optimized salvation radii sufficient to determine biologically interesting properties such as solvent transfer energies, binding energies, pKa shifts, solvent forces, electrostatic descriptors, surface potentials, electrostatic Tanimotos and effective dielectric constants. All parts of the toolkit suite are written in object-oriented C or C++ and are available on Linux, Windows, Mac, and common UNIX flavors, and have a stable, documented application programming interface (API); full-time support staff for timely response to problems and the development of enhancements. This notice of intent is not a request for competitive quotations however, all responses received, within 15 days from the date of publication of this synopsis will be considered by NLM. The quoter shall include all information which documents and/or supports the qualification criteria in one clearly marked section of its quotation. All quotes received within 15 days (August 11, 2004) from the date of publication of this synopsis will be considered by NLM. The contractor shall comply with all applicable Federal, State, and local laws, executive orders, rules and regulations applicable to its performance under this order. Full text of clauses and provisions are available at Federal Acquisition Regulation (FAR): http://www.arnet.gov/far/. Quotes submitted in reference to this requirement must state RFQ-NLM 04-195/KDR on their submission. Quotes must be sent to: National Library of Medicine, Building 38A, Room B1N17, 8600 Rockville Pike, Bethesda, Maryland 20894. Questions in reference to this requirement can be submitted by electronic email messaging to kr33v@nih.gov or cara_calimano@nlm.nih.gov.
- Place of Performance
- Address: National Library of Medicine, Building 38A, Room B1N17, 8600 Rockville Pike, Bethesda, MD
- Zip Code: 20894
- Zip Code: 20894
- Record
- SN00631899-W 20040730/040728211842 (fbodaily.com)
- Source
-
FedBizOpps.gov Link to This Notice
(may not be valid after Archive Date)
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