7 Results Found
  • Comparison of docking packages: performance against the Astex Diverse Set

    In this study we identify which GOLD scoring function performs best for pose prediction and compare GOLD’s performance against other docking packages.

    Last Modified: 14/02/2012 PDF

  • GOLD scoring function performance against the DUD decoy/active set

    ​In this study we identify which scoring function performs best overall for Virtual Screening applications, and which may be best applied to certain target classes.

    Last Modified: 14/02/2012 PDF

  • Deriving a receptor based QSAR model using docking data

    The objective of the study is to demonstrate the utility of using GOLD-derived 3D-parameters along with other external 2D-data to illuminate a quantitative understanding of the SAR of a series of potent serine protease inhibitors. It also serves to highlight the ease with which these various data can be handled and displayed in the fully integrated piece of software, GoldMine.

    Last Modified: 14/02/2012 PDF

  • Validation of Docking Poses via Interaction Motif Searching

    Given a set of docking poses for a single ligand can we separate correct poses from high scoring but incorrect poses by comparing protein-ligand interaction motifs?

    Last Modified: 14/02/2012 PDF

  • Identifying and modelling key water molecules

    Water molecules can play key roles in mediating protein-ligand interactions. In this use case we illustrate how to make the most out the vast amounts of structural data available from the PDB and the CSD when trying to identifying key hydration sites. We will also show how to model water molecules in protein-ligand docking.

    Last Modified: 14/02/2012 PDF

  • Sampling ring conformations during protein-ligand docking

    ​Ring structures commonly form the core of small molecule drugs and biological substrates. The problem of exploring conformational space of flexible rings in protein-ligand docking is examined using the program GOLD.

    Last Modified: 14/02/2012 PDF

  • Improved docking performance using ensemble docking

    In this case study we illustrate the use of ensemble docking in the context of pose prediction and virtual screening .​

    Last Modified: 14/02/2012 PDF