6 Results Found
  • 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

  • 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

  • Identifying new BACE inhibitors from non-homologous structures

    The object of this study is to identify structures in the PDB that have similar cavities in terms of shape and properties to a cavity of known pharmaceutical interest. Any ligands bound to those cavities may well be of interest either in an assay, or as a source of new ideas about possible hybrids or derivatives. ​

    Last Modified: 14/02/2012 PDF

  • Assessing the reliability of protein-ligand structures

    ​A common task in structure-based drug design is the validation of protein-ligand structures. This process needs to be quick, visual and aided by numeric data. Here we present a simple workflow for rapidly detecting suspect and/or interesting features of protein-ligand complexes.

    Last Modified: 14/02/2012 PDF