Homology modeling Modeller tool

MJ Bower, FE Cohen, RL Dunbrack Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library A new homology modeling tool. J Mol Biol 267 1268-1282, 1997. 

However, in many cases the proteins considered in the analysis are very similar and show only little structural variation. In these cases a superimposition of structurally conserved regions with standard protein homology modeling tools has yielded satisfactory protein superimpositions suited for the GRID/PCA or GRID/ GPGA analysis [8,9,13,17]. 

Thus, EcR LBD homology models based on vertebrate nuclear receptor crystal structures, although instructive for general architecture and residue replacement, are, owing to their low sequence identity, rather speculative when used for ligand docking or as tools for virtual screens [164],... 

At about the same time, Terp et al. [11] used GRID/CPCA to analyze 10 MMPs with the intention of highlighting regions that could be potential sites for obtaining selectivity. Some of the structures were retrieved from the RCSB protein data bank [53], others were obtained through homology modeling [56]. To facilitate the analysis, the authors used the cut-out tool to focus on each of the six subsites in turn. 

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