Sub‐angstrom modeling of complexes between flexible peptides and globular proteins

By Barak Raveh, Nir London, O. Schueler‐Furman. 2010

415 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Jeffrey J. Gray
2. Björn Wallner
3. Isak Johansson-Åkhe
4. Sergey Lyskov
5. O. Schueler‐Furman
6. Brian D. Weitzner
7. Barak Raveh
8. Nir London

In Spectroscopy

1. O. Schueler‐Furman
2. Björn Wallner
3. Isak Johansson-Åkhe
4. Barak Raveh
5. Nir London
6. Jeffrey J. Gray
7. Dima Kozakov
8. Philip Bradley

Citations in the corpus

• Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions (2011, methodology): “Rosetta FlexPepDock (14) is a high-resolution protocol for the refinement of peptide-protein complex structures that is implemented in the Rosetta modeling suite framework (15).”
• Harnessing protein folding neural networks for peptide–protein docking (2021, methodology): “Based on this finding, we developed the first high resolution, global blind peptide docking protocol, PIPER-FlexPepDock (PFPD) (21), in which a fragment conformer ensemble extracted from monomer structures (using the Rosetta Fragment Picker, (22)) is used to represent the peptide conformation, exhau”
• Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors (2011, methodology): “For instance, key motif residues may be modeled particularly well, (see our previous analysis in Raveh et al [26]), and other inaccuracies may be introduced by intrinsic motility of flexible peptide tails, and effects due to symmetry related contacts to the peptide that are not taken into account in”
• CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site (2015, neutral): “Computational protein–peptide docking is usually divided into three consecutive steps realized by separate protocols (3): (1) prediction of the binding site(s) on the receptor structure, (2) initial modeling of the peptide backbone in the binding site(s), and finally (3) refinement of the initial pr”
• Improving peptide-protein docking with AlphaFold-Multimer using forced sampling (2021, methodology): “The 250 candidates with the lowest score from each of the conformations are all refined using Rosetta FlexPepDock before being clustered (Raveh et al., 2010).”
• High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock (2017, methodology): “…of peptide-protein interactions, including the prediction of peptide binding sites [7–9], refinement of coarse peptide-protein models [10], folding and docking on a known binding site [11] and most challenging of all, global peptide-protein docking with no prior information about the…”
• A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking (2013, neutral): “FlexPepDock [23] was the first generic algorithm aiming at modeling near-native protein-peptide complexes, starting either from an ensemble of perturbed peptide structures or, with”
• Peptiderive server: derive peptide inhibitors from protein–protein interactions (2016, background): “Such peptides often exhibit calculated binding energies similar to those of known peptide–protein interactions, and tend to retain their binding conformation also out-of-context of the full protein, as demonstrated by FlexPepDock refinement (9) of the derived peptide–receptor complex (6).”