Objectives

Team

Main objective: Describe the main objective of this research (sub)project

Project owner: Chaya Stern (Deactivated) Joshua Horton

Objectives for 2020: Describe the main goals of this research project for 2020 (or the next OFF release)

Team members: David MobleyLee-Ping Wang Daniel Smith (Deactivated) Trevor Gokey Jessica Maat (Deactivated) Hyesu Jang

Scientific Questions

  • What’s the optimal way of doing torsion fitting?

    • When to run multidimensional scans?

    • When torsions need to be split using chemical perception?

    • How to select which torsions to scan? Avoid scanning linear fragments and standardize selection method 

    • Getting phases right

    • Can optimization datasets minimization energy and gradient histories be used as a cheaper alternative to torsion scans?

  • Is the current LJ and 1-4 scaling optimal?

    • Diagnostics for pathological cases / sterics / 1-4 interactions & electrostatics in torsion drive

    • 1-4 interactions turned on or off?

    • Optimal LJ mixing rules?

  • Do we need specific protein backbone torsions? What data?

Infrastructure requirements

Describe what infrastructure is required for this project. Link to the relevant infrastructure page. Tag relevant team members if needed.

QCArchive, torsiondrive, geomeTRIC, Fragmenter, ChemPer, OpenEye, RDKit, AmberTools (WBO?)

Data requirements

What datasets are generated or needed for this project? Link to relevant Confluence, Google drive, Github or Zenodo pages. Tag relevant team members if needed.

QCArchive / Molecule selection