Installation instructions 3DM

Owned by Daniël Brouwer (Unlicensed)
Last updated: Oct 14, 2024 by Femke Kopmels
2 min read

This guide is for registered 3DM users that have a Bio-Prodict account. If you do not have an account yet, please start by filling out the form on the registration page. Are you eligible for an academic license? Make sure to register with your academic email address. Once you submit the registration form, you will receive a confirmation email with further instructions on how to activate your account.

About 3DM

3DM information systems are protein super-family platforms that collect, combine and integrate many different types of protein-related data. They are designed to facilitate the exploration of sequence-structure-function relations which can be useful to, e.g.:

  • Elucidate the function of individual amino acids

  • Predict the effects of mutations for protein optimisation

  • Intelligently design protein panels

  • Investigate the patent landscape for a protein or complete protein family

To get maximum value out of 3DM, we advise you to follow the freely available 3DM Course. The course contains a large practical component in which participants learn to solve real life problems from different fields (protein engineering, homology modeling, and drug design), using our 3DM Systems.

Would you like to learn more about 3DM? Please watch the 3DM Video, read the 3DM Walkthrough and/or consult our publications on the website.

Install a visualization tool

To make full use of the 3DM platform, you need to install a visualization tool (YASARA or PyMol) that runs on your own machine. The links below contain a description on how to install your tool of choice:

Note that the installation of a visualization tools is not necessary to use our 3DM web platform. However, these tools can visualize the structures that you are interested in which may provide new insights. An example of a 3D structure of a protein visualized in YASARA is shown in Figure 1.

image-20241010-112519.png
Figure 1. IA28A visualized in YASARA.

Install the 3DM plugin

To view 3DM data inside protein structures and models, you can install the 3DM plugin for your molecular viewer of choice:

There are numerous options of mapping data onto the structure(s) in your scene. For example, you can project mutation data, ligand contacts, or additional structures. You can learn more about when and how to use the 3DM plugins in the 3DM Walkthrough and our freely available 3DM Course.

Installation problems

Are you facing any problems with your installation? Please consult our Troubleshooting page. In case you can’t find your solution there, please reach out to us!

Bio-Prodict