How to curate/select compounds in Fragalysis

Owned by Max Winokan
Nov 15, 2023
2 min read

N.B. Fragalysis is still in active development so the features shown here may change rapidly

Getting Started

Fragalysis available at https://fragalysis.diamond.ac.uk/

  1. Choose the target you wish to work on

  2. Recap of Fragalysis’ layout

  • Share / upload this allows you to create and share a permanent link to your exact Fragalysis state

  • Tags This is how you can control which hits are visible by sites and other categories

  • LHS / Hits Here you can navigate all the hits and add visualisations to them (The Tags panel also belongs to the LHS)

    • The visualisation buttons are shared also with virtual hits (RHS) and work as follows:

      • All : show ligand in (CPK), protein side chains (lines), and interactions.

      • Ligand: Ligand (CPK)

      • Protein: Protein side chains (lines)

      • Interactions: Interactions

      • Surface: Electrostatic surface of the protein

      • Electron Density: Experimental electron density

      • Vectors: Possible vectors for elaboration

  • Controlling the NGL viewer:

    • Rotate: left click and drag

    • Pan: right click and drag

    • Zoom: scroll

    • 3D Slice: hold shift + scroll

The RHS and curation

The RHS is where follow-up designs and their virtual hits are navigated

Compound set

  • Follow-up designs are uploaded as compound sets and selected via the highlighted dropdown

  • You can use the search and filter functionality to navigate the set

  • Colors

    • You can paint compounds with colours that can be renamed, i.e. “Yes”, “No”, “Maybe”

    • These labels will be assigned to compounds in your session and can be downloaded as a CSV in the “selected compounds” tab

  • Inspirations

    • The “F” button on each compound can be used to bring up a modal with the experimental hits used as inspiration for the compound design

    • The same LHS visualisation buttons are available to superimpose the inspiration hit with the follow-up design

  • Arrows

    • Use these arrows to quickly apply the current visualisations to adjacent compounds

    • This works best when inspirations modal is open, and the inspiration hits and current compound are shown as ligands

The selected compounds tab

Once you have ‘painted’ compounds from different sets they can be viewed together in the “selected compounds” tab

Once the selection is finalised, use the “Download CSV” button to download a CSV of your selections, and share this file with those progressing the order.