Computational chemistry guides & tools

Computational chemistry guides & tools

MMV is part of a network of Product Development Partnerships (PDPs), working together to share knowledge in the area of computational chemistry and cheminformatics, in order to advance drug discovery for neglected tropical diseases. With the support of the Bill & Melinda Gates Foundation, AMG Consultants Ltd has produced a series of guides to share free solutions to common problems faced by medicinal and computational chemists in the not-for-profit arena.

Many computational tools are available to support drug discovery, but they are not always accessible, affordable or user-friendly. Rather than simply generating a list of tools, AMG has identified common tasks in medicinal chemistry and created guides to illustrate how free computational tools can provide practical solutions to real drug discovery problems.

Free tools for medicinal and computational chemists

Tools were chosen to address common needs expressed by medicinal and computational chemists working in the not-for-profit area. Recognising that this is a global effort, we have selected software packages on the basis of being free for all users. Comments and questions on guides and tools are welcome. Please email

Below is a list of guides and tools. Watch a webcast that introduces the following tutorials (29min).

1. PK Tool: a PKPD simulation tool for human PK & dose projection

This is a tool to analyse in vitro & in vivo ADME & PK data. Predictions for human PK & dose can be made based on available data & assumptions about efficacious concentration. Guidance is given on how secure such projections are likely to be given the nature and congruence of the data available. The training materials include theoretical background, slides, video presentations & test data for hands-on exercises.

In early 2022, the source code was developed to add options to help analyse situations where long-acting or extended-release formulations. Explanatory notes, source code & test data are all available

2. Using ligand efficiency metrics to optimise CCR5 antagonists

This guide uses the free tool DataWarrior and demonstrates how to calculate simple physical chemical properties, graph structure-activity data and analyse compound sets with three popular ligand efficiency metrics. A video introduction to DataWarrior (14 min) is also available.  The full guide also demonstrates how to obtain biological data associated with papers from ChEMBL and manipulate data sets in spreadsheets and/or with KNIME.

3. Visualisation and analysis of protein – ligand interactions

This guide describes how to visualize protein–ligand interactions from a crystal structure file (PDB) using the free tool YASARA. It takes you through visualization options, identifying protein–ligand interactions, creating simple surfaces and representing structures in a variety of different ways.

4. Know Your Molecule – a tool to help look at published information about the chemical space around your compounds

Deciding which series to invest synthetic effort in is a key step in drug discovery. One important element of that decision is understanding the known pharmacology of compounds related to your series. This guide uses the free tools KNIME and DataWarrior to search and analyse data from ChEMBL on compounds similar to your input molecules.

Additional resources 

The document above lists some additional resources you may find helpful.


Information on this page is provided by AMG Consultants. The information is advisory only and represents the views of AMG Consultants. The information does not represent the views of MMV nor of the Bill & Melinda Gates Foundation. None of these organisations accept responsibility or liability for the tools or for the consequences of any actions taken on the basis of the information provided on the use of the tools. The information, both the guides and links provided are correct at time of publication. AMG Consultants will make reasonable efforts to maintain the content but accept no liability for any changes to the tools or the free status of those tools at any point in the future. AMG Consultants are aware that other similar tools exist and no favourable or unfavourable opinion should be inferred from the inclusion or exclusion of any particular tool to this website.