Improved side‐chain modeling for protein–protein docking

By Chu Wang, O. Schueler‐Furman, David Baker. 2005

239 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Materials Chemistry

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Citations in the corpus

Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013, methodology): “The continuous, one-at-a-time rotamer optimization protocol is called rtmin (Wang et al., 2005).”
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, positive): “…et al. , 2004; Kuhlman and Baker, 2000) protein_docking Predict the docked conformation of two proteins with a known structure (Gray et al. , 2003; Wang et al. , 2005) ligand_docking Predict the orientation that a small molecule binds to a protein (Davis and Baker, 2009; Kaufmann et al. , 2008;…”
Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics (2010, background): “Currently, Rosetta’s scoring function incorporates various types of physicochemical interactions, such as coulombic charge-charge interactions, hydrogen bonding, van der Waals interactions, desolvation energies, etc. (59, 60).”
Principles of Flexible Protein-Protein Docking (2008, methodology): “113,118”
FireDock: a web server for fast interaction refinement in molecular docking (2008, background): “RosettaDock (12,25) web server allows local search in the vicinity of a single given input solution candidate.”
New algorithms and an in silico benchmark for computational enzyme design (2006, methodology): “We describe two different methods for inside-out method, based on the inverse rotamer tree and an outside-in method called RosettaMatch.”
Flexible protein-protein docking. (2006, unknown): “Recent developments include the sampling of off-rotamer sidechain conformations [34 ] and a new solvated rotamer library [35].”
RosettaAntibody: antibody variable region homology modeling server (2009, methodology): “The high-resolution phase iteratively performs the following: (i) optimizes side chains via rotamer packing and continuous minimization (13), (ii) perturbs CDR backbone torsion angles and the relative orientation of the light and heavy chains, and (iii) uses gradientbased minimization over the CDR t”
Protein-protein docking with backbone flexibility. (2007, unknown): “Periodically, side chains are optimized by combinatorial packing(32) or rotamer trials with minimization.(14) Backbone bond lengths and angles are kept fixed during the simulation.”
FireDock: Fast interaction refinement in molecular docking (2007, background): “The RosettaDock refinement31,32 performs repeated cycles of side-chain optimization and adjustments of the relative orientation of the molecules.”
ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility (2006, unknown): “18,29 In our cross-docking benchmark, 23% of all side-chains in the first and second shell of the binding site change to a different rotamer (Table SII).”
Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2 (2011, methodology): “0u, (2) the rigid-body orientation is energy-minimized, and (3) side-chain conformations are optimized with RotamerTrials [27], followed by a test of the Metropolis criteria.”
Automating human intuition for protein design (2014, methodology): “24 The greedy algorithm applied to the protein design problem is most similar to the Self-Consistent Mean-Field method25,26 but with mutations applied in rank order, and without iteration or a check for self-consistency.”