Protein–protein docking with a reduced protein model accounting for side‐chain flexibility

By Martin Zacharias. Protein Science, 2003

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Improved side‐chain modeling for protein–protein docking (2005, neutral): “Copyright © 2005 The Protein Society1328 docking using a reduced protein model (Vakser et al. 1999; Zacharias 2003) or softened protein surfaces (Gabb et al. 1997; Palma et al. 2000) to allow some tolerance of atomic clashes across protein interfaces.”
Principles of Flexible Protein-Protein Docking (2008, methodology): “These methods can be divided into three major groups: (i) brute force techniques66–68 that can be significantly speeded up by FFT,69–74 (ii) randomized methods10,75 and (iii) shape complementarity methods.”
Flexible protein-protein docking. (2006, positive): “ATTRACT [31,32] uses a reduced protein representation together with multiple sidechain copies: switching between rotamers is performed at various stages during docking and the best conformation is selected for the next few subsequent EM steps.”
MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15–19 (2010, methodology): “17,16 The initial binding poses by the FFT method are filtered by a shape complementarity criterion, leaving usually several thousands poses to be further refined by a recent iteratively-derived knowledge-based scoring function (ITScorePP).”