SOW.pdf

Sol No.: 75F40119Q00071

Statement of Work (SOW)

Title: Schrödinger Suite License Renewal – Chemical Simulation Software – Small Molecule Drug Discovery Suite

1. Background

The Division of Bioinformatics and Biostatistics (DBB) of the National Center for Toxicological Research (NCTR) of the Food and Drug Administration (FDA) is currently conducting research in computational chemistry. A crucial component of the research involves chemical structure analysis. We require the latest generation of chemical simulation software to provide us with comprehensive tools required for analysis of chemical structures, and quantitative structure-activity relationships (QSARs), as well as visual graphics, to enable our efforts in computational chemistry. The DBB has been utilizing the Schrödinger Suite chemical simulation software (Small Molecule Drug Discovery Suite) since 2012 at a cost of $230,000 to date. Other software suites were researched for compatibility, but were not as flexible, did not fit the requirement fully, and would not produce the results necessary for the project.

The Schrödinger Suite chemical simulation software licenses (Small Molecule Drug Discovery Suite) are up for renewal. If these licenses are not renewed, the research in computational chemistry will be negatively impacted, as it will preclude NCTR’s ability to continue the ongoing project that needs computational chemistry.

2. Objective

Renewal of Schrödinger Small Molecule Drug Discovery Suite license for the period of July 16, 2019, through July 15, 2020. Renewal of the current licensing is the most cost-effective alternative as well as least disruptive.

3. Requirements

3.1 The Schrödinger Suite is a comprehensive package of chemical simulation software engineered specifically for pharmaceutical and biotechnology research. The predictive power of Schrödinger’s software accelerates research and development activities and provides the precision tooling for the analysis needed to support our research endeavors.

3.2 Software License Requirements (Salient Characteristics)

To be considered for award, the Contractor shall provide 25 Tokens (interchangeable licenses) which will allow DBB to run any combination of programs in the interchangeable library up to the total number of tokens available in the library at any given time. The programs should be able to be run by one or more users, as long as they don’t exceed 25 tokens. Once the programs finish, the tokens shall be returned to the license manager and available for additional programs -

- either by the same user or multiple users.

Salient functional characteristics:

1. Contractor shall provide an interchangeable library to include the following:

Small-Molecule Drug Discovery Suite

Software application Description

AutoQSAR automatically creates Quantitative Structure-Activity Relationship (QSAR) models that can be validated and employed within Maestro

Canvas

QSAR and cheminformatics (comprehensive cheminformatics computing environment). Extensive access to tools for property calculations, clustering, diversity, classification, QSAR, and data reduction.

ConfGen bioactive conformational searching

Core Hopping attachment and shape-based scaffold hopping

Desmond Molecular Dynamics simulations for biomolecular systems (Supported on Linux only)

Desmond GPU Molecular Dynamics simulations for biomolecular systems (Supported on GPU only)

Epik pKa calculation in biological conditions

Field-based QSAR quantitative predictions of binding-site chemistry

Glide ligand-receptor docking (requires 6 tokens when run with XP Descriptors on)

Jaguar ab initio quantum mechanics application

Jaguar pKa Ab initio pKa prediction

LigPrep a 2D to 3D conversion program to prepare ligand libraries

MacroModel classical molecular modeling application

Membrane Permeability

Physics-based, accurate predictions of passive membrane permeability

P450 SOM Prediction workflow to calculate likely sites of metabolism by 2D6 or 2C9 P450 isoform.

Phase ligand-based pharmacophore modeling

Prime protein structure prediction package

PrimeX protein crystal structure refinement

QikProp ADME properties prediction of drug candidates

QSite High performance QM/MM application

Shape Screening shape-based searching and flexible ligand superposition

SiteMap identification and characterization of active sites

Strike scientific data analysis program

XP Visualizer

Displays Glide XP Docking results, provides 3D visualization for XP terms, and allows selective evaluation of ligands within a table

2. Contractor shall provide 25 Tokens (Interchangeable licenses) for use of any program of the software at a given time.

3. Contractor shall provide Maestro Access License - a versatile modeling environment.

4. Contractor shall provide KNIME Access License - A modular, highly configurable framework for easy workflow automation and data analysis.

5. Contractor shall provide OPLS3 Force Field Access License - force field with the most comprehensive coverage of chemical space.

6. All software shall be Windows 7 64-bit compatible, and Windows 10 64-bit compatible.

4. Specific Tasks/Deliverables

Product Description Qty Unit of Issue

Period of Performan ce

Uni t

Pric e

Total Price

BASE YEAR

Ref.

Schrödinger Suite chemical simulation software: (Small Molecule Drug Discovery Suite (part number not available) interchangeable library including AutoQSAR, Canvas, ConfGen, Core Hopping, Desmond, Desmond GPU, Epik, Fieldbased, QSAR, Glide, Jaguar, Jaguar pKa, LigPrep, MacroModel, Membrane Permeability, P450 SOM Prediction, Phase, Shape Screening, Prime, PrimeX, QikProp, QSite, SiteMap, Strike, XP Visualizer.

1 each 7/16/2019 – 7/15/2020

Interchangeable licenses (allowing multiples users/programs at one time)

25 token s

7/16/2019 – 7/15/2020

Maestro Access License 1 each 7/16/2019 – 7/15/2020

KNIME Access License 1 each 7/16/2019 –

OPLS3 Force Field Access License

All software shall be Windows 7 64-bit compatible, and Windows 10 64-bit compatible.

1 each 7/16/2019 –

64-bit compatible, and Windows 10 64-bit compatible.

1 each 7/16/2019 –

OPTION YEAR 1

Ref.

Schrödinger Suite chemical simulation software: (Small Molecule Drug Discovery Suite) interchangeable library including AutoQSAR, Canvas, ConfGen, Core Hopping, Desmond, Desmond GPU, Epik, Fieldbased, QSAR, Glide, Jaguar, Jaguar pKa, LigPrep, MacroModel, Membrane Permeability, P450 SOM Prediction, Phase, Shape Screening, Prime, PrimeX, QikProp, QSite, SiteMap, Strike, XP Visualizer.

1 each 7/16/2020 – 7/15/2021 time)

25 token s

7/16/2020 – 7/15/2021

Maestro Access License 1 each 7/16/2020 – 7/15/2021

KNIME Access License 1 each 7/16/2020 – 7/15/2021

OPLS3 Force Field Access License 1 each 7/16/2020 – 7/15/2021

64-bit compatible.

1 each 7/16/2020 – 7/15/2021

OPTION YEAR 2

Ref.

Schrödinger Suite chemical simulation software: (Small Molecule Drug Discovery Suite) interchangeable library including AutoQSAR, Canvas, ConfGen, Core Hopping, Desmond, Desmond GPU, Epik, Fieldbased, QSAR, Glide, Jaguar, Jaguar pKa, LigPrep, MacroModel, Membrane Permeability, P450 SOM Prediction, Phase, Shape Screening, 1 each 7/16/2021 – 7/15/2022

Prime, PrimeX, QikProp, QSite, SiteMap, Strike, XP Visualizer.

time)

25 token s

7/16/2021 – 7/15/2022

Maestro Access License 1 each 7/16/2021 – 7/15/2022

KNIME Access License 1 each 7/16/2021 – 7/15/2022

OPLS3 Force Field Access License 1 each 7/16/2021 – 7/15/2022

64-bit compatible.

1 each 7/16/2021 – 7/15/2022

OPTION YEAR 3

Ref.

Schrödinger Suite chemical simulation software: (Small Molecule Drug Discovery Suite) interchangeable library including AutoQSAR, Canvas, ConfGen, Core Hopping, Desmond, Desmond GPU, Epik, Fieldbased, QSAR, Glide, Jaguar, Jaguar pKa, LigPrep, MacroModel, Membrane Permeability, P450 SOM Prediction, Phase, Shape Screening, Prime, PrimeX, QikProp, QSite, SiteMap, Strike, XP Visualizer.

1 each 7/16/2022 – 7/15/2023 time)

25 token s

7/16/2022 – 7/15/2023

Maestro Access License 1 each 7/16/2022 – 7/15/2023

KNIME Access License 1 each 7/16/2022 –

OPLS3 Force Field Access License 1 each 7/16/2022 –

64-bit compatible.

1 each 7/16/2022 –

5. Inspection and Acceptance

The Contracting Officer’s Representative or Technical point of contact will perform inspection and acceptance of products to be provided. All deliverables shall be provided in accordance with the dates provided in the deliverables table.

Completion of all deliverables, quality and timeliness of delivery, as well as incidents and types of defects, will be used to evaluate the Contractor’s progress and suitability.

FDA will load the software and licensing to verify that the media is functioning properly. The Government shall have 10 working days to inspect and verify that the software is operational, functional and compatible with FDA server and software.

6. Delivery location

The Contractor shall install/renew all software licenses and relevant documentation, electronically on workstations located at:

US FDA

National Center for Toxicological Research 3900 NCTR Road, Jefferson, AR 72079

7. Contract Type

The contract type for this Task Order is Firm-Fixed-Price.

8. Period of Performance

The Period of Performance shall be as follows:

Base Year: July 16, 2019, through July 15, 2020.

Option 1: July 16, 2020, through July 15, 2021.

Option 2: July 16, 2021, through July 15, 2022.

Option 3: July 16, 2022, through July 15, 2023.

9. Other Pertinent Information or Special Considerations

Section 508 Standards (Form FDA 4042 - FDA Best Meets Exception attached for Schrodinger)

(a) Pursuant to Section 508 of the Rehabilitation Act of 1973 (29 U.S.C. 794d), as amended by the Workforce Investment Act of 1998, all electronic and information technology (EIT) supplies and services developed, acquired, or maintained under this contract or order must comply with the “Architectural and Transportation Barriers Compliance Board Electronic and Information Technology (EIT) Accessibility Standards” set forth by the Architectural and Transportation Barriers Compliance Board (also referred to as the “Access Board”) in 36 CFR part 1194. Information about Section 508 is available at http://www.hhs.gov/web/508. The complete text of Section 508 Final Provisions can be accessed at http://www.access-board.gov/guidelines- and-standards/communications-and-it/about-the-section-508-standards.

(b) The Section 508 accessibility standards applicable to this contract or order are identified in the Statement of Work or Specification or Performance Work Statement. The contractor must provide any necessary updates to the submitted HHS Product Assessment Template(s) at the end of each contract or order exceeding the simplified acquisition threshold (see FAR 2.101) when the contract or order duration is one year or less. If it is determined by the Government that EIT supplies and services provided by the Contractor do not conform to the described accessibility standards in the contract, remediation of the supplies or services to the level of conformance specified in the contract will be the responsibility of the Contractor at its own expense.

(c) The Section 508 accessibility standards applicable to this contract are:

• E101.2 Equivalent Facilitation (Appendix A, Application and Scoping Requirements)

• E203 Access to Functionality (Appendix A, Application and Scoping Requirements)

• E204 Functional Performance Criteria (Appendix A, Application and Scoping

Requirements)

• E205 Electronic Content (Appendix A, Application and Scoping)

• 302 Functional Performance Criteria (Appendix C, Application and Scoping

Requirements)

• E207 Software (Appendix A, Application and Scoping Requirements)

• Chapter 5 Software (Appendix C)

(d) In the event of a modification(s) to this contract or order, which adds new EIT supplies or services or revises the type of, or specifications for, supplies or services, the Contracting Officer may require that the contractor submit a completed HHS Section 508 Product Assessment Template and any other additional information necessary to assist the Government in determining that the EIT supplies or services conform to Section 508 accessibility standards. Instructions for documenting accessibility via the HHS Section 508 Product Assessment Template may be found under Section 508 policy on the HHS website:

(http://www.hhs.gov/web/508). If it is determined by the Government that EIT supplies and https://www.hhs.gov/web/508 http://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-section-508-standards http://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-section-508-standards http://www.access-board.gov/guidelines-and-standards/communications-and-it/about-the-section-508-standards http://www.ecfr.gov/cgi-bin/text-idx?node=pt48.1.2&se48.1.2_1101 https://www.hhs.gov/web/508 services provided by the Contractor do not conform to the described accessibility standards in the contract, remediation of the supplies or services to the level of conformance specified in the contract will be the responsibility of the Contractor at its own expense.

(e) If this is an Indefinite Delivery contract, a Blanket Purchase Agreement or a Basic Ordering Agreement, the task/delivery order requests that include EIT supplies or services will define the specifications and accessibility standards for the order. In those cases, the Contractor may be required to provide a completed HHS Section 508 Product Assessment Template and any other additional information necessary to assist the Government in determining that the EIT supplies or services conform to Section 508 accessibility standards.

Instructions for documenting accessibility via the HHS Section 508 Product Assessment Template may be found at http://www.hhs.gov/web/508. If it is determined by the Government that EIT supplies and services provided by the Contractor do not conform to the described accessibility standards in the provided documentation, remediation of the supplies or services to the level of conformance specified in the contract will be the responsibility of the Contractor at its own expense.

10. Government Point of Contact

Contracting Officer’s Representative

Tramon Henry U.S. Food and Drug Administration Office of Information Management and Technology Lacinda Welch, 3900 NCTR Rd., Jefferson AR 72079 Lacinda.welch@fda.hhs.gov

Contract Specialist

Erika Crawford U.S. Food and Drug Administration Office of Acquisitions & Grants Services 4041 Powder Mill Rd, Beltsville, MD 20705 Erika.Crawford@fda.hhs.c om

The COR may be changed at any time by the Government without prior notice to the Contractor by a unilateral modification to the Contract. The responsibility and limitation of the COR are as follows: (1) The COR is responsible for the technical aspects of the project and serves as the technical liaison with the Contractor. The COR is also responsible for the final inspection and acceptance of all reports, and such other responsibilities as may be specified in the contract. (2) The COR is not authorized to make any commitments or otherwise obligate the Government or authorize any changes which affect the Contract price, terms or conditions. Any Contractor request for changes shall be referred to the Contraction Officer directly or through the COR. No such changes shall be made without the expressed prior authorization of the Contracting Officer (CO). The CO may designate assistant or alternate COR to act for the COR by naming such assistant/alternate(s) in writing and transmitting a copy of such designation to the Contractor.

https://www.hhs.gov/web/508

11. Contracting Officers Authority

The Contracting Officer (CO) is responsible for ensuring the performance of all necessary actions for effective contracting; ensuring compliance with the terms of the contract and safeguarding the interests of the United States in its contractual relationships. The CO is the only individual who has the authority to enter into, administer, or terminate this contract and is the only person authorized to approve changes to any of the requirements under this contract, and notwithstanding any provision contained elsewhere in this contract, this authority remains solely with the CO.

No statement, whether oral or written, by anyone other than the Contracting Officer, shall be interpreted as modifying the terms and conditions of this award. It is the Contractor’s responsibility to contact the CO immediately if there is even the appearance of any technical direction that is or may be outside the scope of the contract. The Government will not reimburse the Contractor for any work not authorized by the CO, including work outside the scope of the contract.

12. Provisions and Clauses

52.217-9 Option to Extend the Term of the Contract

The Government may require continued performance of any services within the limits and at the rates specified in the contract. These rates may be adjusted only as a result of revisions to prevailing labor rates provided by the Secretary of Labor. The option provision may be exercised more than once, but the total extension of performance hereunder shall not exceed 6 months. The Contracting Officer may exercise the option by written notice to the Contractor within five (5) years.

The below Federal Acquisition Regulation (FAR) Clauses apply. FAR Clauses can be viewed in full text at: https://www.acquisition.gov/browse/index/far

52.203-19 Prohibition on Contracting with Entities that Require Certain Internal Confidentiality Agreements or Statements-Representation (Jan 2017)

52.204-23 Prohibition on Contracting for Hardware, Software, and Services Developed or Provided by Kaspersky Lab and Other Covered Entities (Jul 2018)

52.227-19 Commercial Computer Software License (Dec 2007)

52.232-39 Unenforceability of Unauthorized Obligations (Jun 2013)

52.232-40 Providing Accelerated Payment to Small Business Subcontractors (Dec 2013)

The below Health and Human Services Acquisition Regulation (HHSAR) Clauses apply.

HHSAR Clauses can be viewed in full text at:

http://www.hhs.gov/policies/hhsar/subpart352.html#subpart352.1- InstructionsforUsingProvisionsandClauses

352.203-70 Anti-Lobbying (Dec 2015)

352.211-3 Paperwork Reduction Act (Dec 2015)

352.222-70 Contractor Cooperation in Equal Employment Opportunity Investigations (Dec 2015)

352.224-71 Confidential Information (Dec 2015)

352.239-74 electronic Information and Technology Accessibility Notice (Dec 2015)

13. Award Basis

The FDA will evaluate quotes received in response to this RFQ on a lowest price-technically-acceptable basis. A technically acceptable quote is one that offers to provide the FDA with the goods and services specified in this Statement of Work - or functionally equivalent goods that meets all the salient characteristics and requirements of this SOW – within the specified delivery schedule.

http://www.hhs.gov/policies/hhsar/subpart352.html#subpart352.1--InstructionsforUsingProvisionsandClauses http://www.hhs.gov/policies/hhsar/subpart352.html#subpart352.1--InstructionsforUsingProvisionsandClauses http://www.hhs.gov/policies/hhsar/subpart352.html#subpart352.1--InstructionsforUsingProvisionsandClauses http://www.hhs.gov/policies/hhsar/subpart352.html#subpart352.1--InstructionsforUsingProvisionsandClauses