176 Results Found
  • 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

  • Scaffold-hopping and fragment-linking using the Cambridge Structural Database

    ​In this study we illustrate use of the Cambridge Structural Database to provide ideas for novel scaffolds giving an active inhibitor of known binding mode. Also, we identify good linkers between two fragments binding in different parts of the active site.

    Last Modified: 14/02/2012 PDF

  • Integrating Relibase+ information with other data sources

    ​We illustrate how a major pharmaceutical company integrated structural information from Relibase+1 into their Phylosopher2 database. The aim was to make structural data available to researchers in target discovery via the Phylosopher interface.

    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

  • Validating protein-bound metals

    ​We compare the structure of a protein-bound metal and its coordination shell, with similar coordination structures in the CSD. This analysis may be useful in identifying errors in metal assignment or in coordination geometry in X-Ray derived protein models.

    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

  • Designing a New Multi-Component API Form Based on a Known Structure

    This use case addresses the topic of how to design new multi-component, crystalline forms of an API purely based on the knowledge of one or more existing forms. The production of new multi-component forms will allow the physico-chemical properties of the solid to be modified (e.g. solubility, crystal habit and stability) without changing the biological efficacy of the API compound. If an isostructural series of API forms can be generated in this way, then tuning of physical properties may even be feasible.

    Last Modified: 14/02/2012 PDF