Shape complementarity at protein–protein interfaces

By Raquel Norel, Shuo-liang Lin, Haim J. Wolfson, Ruth Nussinov. 1994

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Citations in the corpus

AbDesign: an algorithm for combinatorial backbone design guided by natural conformations and sequences (2015, unknown): “58 implemented in Rosetta.”
Protein interaction interface region prediction by geometric deep learning (2021, background): “Scoring functions are often carefully crafted to integrate multiple factors, with shape complementarity as the foundation (Lawrence and Colman, 1993).”
Finding correct protein–protein docking models using ProQDock (2016, unknown): “formation, like shape complementarity (Lawrence and Colman, 1993) while on the other end, there could be features that might largely vary even among good-quality models.”
Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles (2015, background): “The tested set of potentials includes: the all-atom empirical potential FoldX [42, 43], a composite statistical and physics based potential from Rosetta (Talaris 2013) [44], residue and all-atom docking potentials (PIE [45] and PISA [46], respectively), all atom and Cβ based statistical potentials (”
Protein–protein interaction and quaternary structure (2008, background): “Table 2 lists two other parameters related to the atomic packing : the LD packing index of Bahadur et al. (2004) and the Sc shape complementarity score of Lawrence & Colman (1993).”
Mechanism of activation and inhibition of the HER4/ErbB4 kinase. (2008, background): “The ErbB4 asymmetric dimer buries 2252 Å2 with a shape complementarity value of .657 (Lawrence and Colman, 1993).”
Principles of docking: An overview of search algorithms and a guide to scoring functions (2002, methodology): “We further note that, in principle, the Geometric Hashing can handle any type of molecular surface representation.”
Structural basis for inhibition of the epidermal growth factor receptor by cetuximab. (2005, methodology): “The structure described here represents the first structure of sEGFR with no body-antigen binding interface (Lawrence and Colman, 1993), but is similar to that observed for the interaction of sErbB2 with bound growth factor ligand and at neutral pH.”
P HYSICS - INFORMED DEEP NEURAL NETWORK FOR RIGID - BODY PROTEIN DOCKING (2022, methodology): “The surface shape-complementarity of two proteins bound to each other is a well documented phenomena (Lawrence & Colman, 1993; Jones & Thornton, 1996) and has been widely used in classical methods for protein-protein docking (Gabb et al., 1997; Chen & Weng, 2002; Duhovny et al., 2002; Comeau et…”