ConSeq: the identification of functionally and structurally important residues in protein sequences

By C. Berezin, Fabian Glaser, J. Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, Rita Casadio, Nir Ben-Tal. Bioinform., 2004

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3DLigandSite: predicting ligand-binding sites using similar structures (2010, background): “Sequence conservation is commonly used to predict binding sites (2,3).”
Prediction‐based fingerprints of protein–protein interactions (2006, background): “19,31 However, because of the lack of accurate characterization of the surface geometry and the additional uncertainty introduced by RSA predictions, 35,50 it remains to be seen if significant progress can be made without incorporating experimentally derived (or obtained using reliable modeling…”
Assessment of ligand binding residue predictions in CASP9 (2011, background): “…suggest changes in the format of the experiment to overcome the current limitations of the assessment. from sequence, based on sequence conservation,2–7 geometric criteria of the protein surface,8–12 or homology transfer from known structures.13 –17 The function prediction category (FN) was…”