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Proteins. 2014 Dec;82(12):3255-72. doi: 10.1002/prot.24658. Epub 2014 Oct 30.

Detecting local residue environment similarity for recognizing near-native structure models.

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Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47906.


We developed a new representation of local amino acid environments in protein structures called the Side-chain Depth Environment (SDE). An SDE defines a local structural environment of a residue considering the coordinates and the depth of amino acids that locate in the vicinity of the side-chain centroid of the residue. SDEs are general enough that similar SDEs are found in protein structures with globally different folds. Using SDEs, we developed a procedure called PRESCO (Protein Residue Environment SCOre) for selecting native or near-native models from a pool of computational models. The procedure searches similar residue environments observed in a query model against a set of representative native protein structures to quantify how native-like SDEs in the model are. When benchmarked on commonly used computational model datasets, our PRESCO compared favorably with the other existing scoring functions in selecting native and near-native models.


decoy selection; protein local structures; protein structure models; quality assessment; residue depth; residue environment

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