Rafi Najmanovich

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Ligand binding may involve a wide range of structural changes in the receptor protein, from hinge movement of entire domains to small side-chain rearrangements in the binding pocket residues. The analysis of side chain flexibility gives insights valuable to improve docking algorithms and can provide an index of amino-acid side-chain flexibility potentially(More)
We present a method to derive contact energy parameters from large sets of proteins. The basic requirement on which our method is based is that for each protein in the database the native contact map has lower energy than all its decoy conformations that are obtained by threading. Only when this condition is satisfied one can use the proposed energy(More)
Upon reanalysis of these data, we found a number of mistakes and realized that salient details were missing from the Materials and Methods section. In particular, once we corrected mistakes in the annotation, we found that the total number of distinct genes that were sequenced from each species actually ranged from 89 to 100. In the analysis, we excluded 7E(More)
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