Identifying targets for bioreductive agents: using GRID to predict selective binding regions of proteins

Computational Methods in Drug Discovery

“…The Q-SITEFINDER (Laurie and Jackson, 2005) algorithm calculates the Van der Waals interaction energy for aliphatic carbon probes on a grid and retains pockets with favorable interactions. The GRID (Reynolds et al, 1989;Wade et al, 1993) algorithm samples the potential on a 3D grid to determine favorable binding positions for different probes. GRID determines interaction energy as a sum of Lennard-Jones, Coulombic, and hydrogen-bond terms.…”

Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials

“…Back-projection of interesting features into the protein structure could be used for visualization and interpretation [46]. Improvement of the presented method could come from the implementation of a larger number of either knowledge-based [9,10] or GRID-like probes [6]. Differentiation between significant and non-significant fields might be sometimes problematic by using just the simple difference fields [4].…”

“…These fields were calculated, e.g. with the GRID program [6] using probes whose interaction energies are defined by empirical force fields. Non-grid-based mapping of protein sites has been performed, e.g.…”

Using Molecular Modelling to Study Interactions Between Molecules with Biological Activity

“…The program GRID [Goodford, 1985] identifies likely protein binding sites for ligands [Reynolds et al, 1989;Cruciani & Goodford, 1994] using a 3D grid around the protein. GLIDE software [Friesner et al, , 2006Halgren et al, 2004] also uses a grid-based scheme to represent the shape and properties of the receptor and then uses a systematic search algorithm to produce a set of initial conformations, using a OPLS-AA force field for ligand minimisation in the field of the receptor.…”