Protein docking for low-resolution structures.

By Ilya A. Vakser. 1995

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Citations in the corpus

Protein docking using spherical polar Fourier correlations (2000, methodology): “24,25 Another attractive feature of this method is that one can perform fast low-resolution searches, for example, to estimate main-chain complementarity 26 and to locate a ligand near a receptor-binding site.”
Protein-protein docking: from interaction to interactome. (2014, unknown): “At lower levels of structural resolution, the difference between unbound and bound conformations is less significant (24,25), and ultimately disappears at ultralow (but still structurally meaningful) resolution (15,24,26).”
Efficient Unbound Docking of Rigid Molecules (2002, methodology): “Most of these methods [33,30,31,32,11,2,3] use brute force search for the 3 rotational parameters and the FFT (Fast Fourier Transform, [19]) for fast enumeration of the translations.”
Dockground: A comprehensive data resource for modeling of protein complexes (2018, methodology): “For each of the 396 unbound–unbound complexes from D OCKGROUND benchmark 4, we generated 300,000 low-resolution docking solutions by GRAMM 51,52 with the grid step 3.5 A˚ and 10 8 angular interval.”
Protein–protein docking benchmark version 4.0 (2010, background): “2IDO_A:B O 1J54_A DNA polymerase III e exonuclease domain 1SE7_A(1) HOT protein (P1 phage) 2.”
Principles of docking: An overview of search algorithms and a guide to scoring functions (2002, methodology): “36,43,44,78,113,142,144–146 In all methods, the search part creates a population of solutions, each assessed by some energy function, whether coarse (e.g., as in rigid-body, or hinge-bending algorithms; Sandak et al. 104 ) or more rigorous (as in MC, MD, simulated optimization).”
Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model. (2018, methodology): “We tested how well our contact potentials score the low-resolution docking predictions by GRAMM (72,73) (Figs.”
Recent progress and future directions in protein-protein docking. (2008, methodology): “…approaches such as threading, phylogenetic profiling, gene neighbourhood and gene fusion analysis, and in silico two-hybrid methods are being used with increasing success to predict PPIs directly from gene sequences of yeast and other organisms (for recent reviews see e.g., references [8-13]).”