Introduction

This section attempts to introduce the uninformed to the main ideas behind the software and clarify some terminology used in the documentation. You can freely skip this section, if you are already familiar with Molpher and molecular morphing.

What is Molpher?

In early stages of any drug discovery endeavor a large library of compounds often needs to be screened for molecules that have the potential to become a new lead in the project. This is usually done in a laboratory setting using a technique called high-throughput screening (HTS). HTS can be a very effective method, but is still very limiting in the number of compounds that can be screened when we consider the incredible vastness of chemical space.

Molpher is a tool developed for the purpose of finding novel active compounds for synthesis/purchase and subsequent testing in drug discovery projects. It is capable of generating a library of potentially active compounds by connecting known active molecules with a chemical space path. Just like any path, a chemical space path has a start and a destination. However, in chemical space this means a source molecule and a target molecule. The path is then just a sequence of structures that connect the two (see chemical space path for more details).

The main motivation to generate such a path is that some new interesting compounds might be discovered along the way. The ones in the middle of the path are usually structurally different from both the source and the target, but at the same time combine their structural features, thus, some of them may form a good basis for a new drug.

Note

If you want to know more about how the algorithm works, read The Morphing Algorithm section of the tutorial.

What is Molpher-lib?

Molpher itself is aimed at users that might use it in their day to day practice to generate focused virtual libraries of compounds. However, there are many possible implementations of the search and many aspects of the exploration could be parametrized. Thus, came the motivation to develop a more flexible and extensible solution that would give everyone an opportunity to easily implement their own ideas or just easily integrate molecular morphing in their existing solutions.

To make it as easy as possible to get up to speed with the library, we have prepared a tutorial in the next section which contains information on how to install and use the library as well as a few example implementations of exploration algorithms using the library.