TY - JOUR
T1 - Normal Modes Expose Active Sites in Enzymes
AU - Glantz-Gashai, Yitav
AU - Meirson, Tomer
AU - Samson, Abraham O.
N1 - Publisher Copyright:
© 2016 Glantz-Gashai et al.
PY - 2016/12
Y1 - 2016/12
N2 - Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes.
AB - Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes.
UR - http://www.scopus.com/inward/record.url?scp=85007579864&partnerID=8YFLogxK
U2 - 10.1371/journal.pcbi.1005293
DO - 10.1371/journal.pcbi.1005293
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C2 - 28002427
SN - 1553-734X
VL - 12
JO - PLoS Computational Biology
JF - PLoS Computational Biology
IS - 12
M1 - e1005293
ER -