PELE Platform features

PELE Platform 1.6 is here

PELE Platform is a suite of packages that aims to find novel solutions to drug discovery problems in a matter of hours. We are constantly improving and developing new features, and we have just released a new version! The new release of the PELE Platform contains many new features and stability changes.

New features

  • FragPELE Libraries. Provide us with a PDB or SD file containing your fragments library and we will enumerate all possible ligands, grow them inside your binding site and rank them from best to worst, always taking receptor flexibility into account. Learn how to grow a custom library.
  • Open Force Field integration. This new release lets you parametrize your ligands and cofactors using Open Force Field as well as the good old OPLS2005 (which remains the default). On top of that, you get to choose the charge parametrization method! Find out how it works.
  • Constraints. We introduced predetermined carbon alpha constraints levels to facilitate the choice of parameters depending on the type of simulation you are running. Additionally, you can now constrain the core of your ligand with a SMILES or SMARTS pattern!
  • Brand new analysis. We give users more flexibility and tools to simplify the analysis of PELE simulations. You can now choose your preferred clustering method, its parameters and criteria to extract most promising structures. We also improved the plots and added information about the water clusters resulting from aquaPELE simulations. Find out more!
  • Covalent docking. We have developed a covalent docking protocol to let you explore all those ligands that covalently bind your target. All you have to do is provide the platform with a ligand covalently attached to the required protein residue and it will sample local conformations to optimize the interactions for you. Follow this tutorial to set up your own simulation.
  • Interaction restrictions. With the new release, you will be able to restrict the interactions between the ligand and the protein by specifying a custom H-bond distance or angle range between selected atoms. Click here for more details.
  • New built-in plotter. A brand new plotter to quickly visualise the progress of your simulation using the command line. You can choose from a number of customizable scatter, density and interactive plots. Give it a try!

  • Conformation perturbation. If you provide PELE with a conformation library, it will perform an additional perturbation step focused on changing the conformation of your ligand. Especially useful if you want to focus on bioactive conformers only or to apply specific sampling to tricky compounds like macrocycles or heterocyclic compounds. Find out more.
  • Singularity. From now on, we support launching PELE from Singularity containers to save some of the trouble with dependencies and compatibility.

To get more information about this release, please check out this link. You can also refer to our documentation to find out how PELE Platform works or send us an email.