# Drug Design Exemplar

Initial Publication Date: March 6, 2014

## Summary

An important problem in the biological sciences is that of drug design. The goal is to find small molecules, called

*ligands*, that are good candidates for use as drugs. The real-world problem is fairly complex. Here we simplify it somewhat to present the essence of the problem being solved. We call this problem description and it solutions an*exemplar*of the original real-world computation. In two documents we provide the following:

- An introduction to the problem and one form of sequential programmed solution.
- Multiple parallel programming solutions using different languages and computing hardware and software.

- Discussion of performance issues to be aware of in the parallel solutions.
- A description of the parallel programming design patterns used in the solutions.

## Learning Goals

- Students will appreciate how parallel program solutions can be used on real-world applications.

- Students will be able to compare running versions of sequential and parallel solutions.
- Students will explore parallel design patterns used in somewhat complex example code.

## Context for Use

These examples would likely be used with students who have some coding experience and feel comfortable with the use of data structures such as vectors and queues.

## Description and Teaching Materials

The web-based version of this module, called Drug Design in Parallel, contains:

- A Drug Design Exemplar description, where the problem domain is described, and
- An initial sequential solution is described, and
- Several different parallel solutions that are compared.

If you want to edit the module yourself, we provide the following versions:

latex tarball of this module, including a pdf file.

MS Word docx version of this module.

## Assessment

Future plans include more suggested homework problems. The module material itself contains guided activities for the students with questions.

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*Drug Design Exemplar*