Efficient docking of peptides to proteins without prior knowledge of the binding site

By C. Hetényi, D. van der Spoel. Protein Science, 2002

455 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/4f00abd926bfd14e6cfa8e864c2c401872c5b699

How researchers see this paper

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

In Computational Theory and Mathematics

1. Garrett M. Morris
2. D. van der Spoel
3. C. Hetényi
4. Arthur J. Olson
5. Ruth Huey
6. Chee Keong Kwoh
7. Yuguang Mu
8. Amr Alhossary

In Molecular Biology

1. Garrett M. Morris
2. O. Schueler‐Furman
3. Arthur J. Olson
4. D. van der Spoel
5. C. Hetényi
6. Ruth Huey
7. Barak Raveh
8. Nir London

In Radiology, Nuclear Medicine and Imaging

1. Ruth Huey
2. Garrett M. Morris
3. Arthur J. Olson
4. C. Hetényi
5. D. van der Spoel
6. O. Schueler‐Furman

Citations in the corpus

• A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking (2013, unknown): “Initial applications focused on specific protein families or domains involved in peptide recognition [2,17– 20], or were restricted to very short peptides [21].”
• CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site (2015, unknown): “To our knowledge, such an approach to docking, without prior knowledge of the binding site, has been successful so far only when applied to very short peptides (2–4 amino acids) (4).”
• Using AutoDock for Ligand‐Receptor Docking (2008, methodology): “AutoDock has been shown to be useful for so-called blind docking (Hetenyi and van der Spoel, 2002, 2006), where the binding pocket is not known, and this is where an alternative, third-party GUI called Blind Docking Tool (BDT; Vaque et al., 2006), can be used to help set up the grid maps required…”
• Protein-Ligand Blind Docking Using QuickVina-W With Inter-Process Spatio-Temporal Integration (2017, background): “In their paper, Hetenyi, and Van Der Spoel recommended a number of trials to exceed 100 times, and at least 10 million energy evaluations per trial in case of flexible ligands 10 .”
• CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting (2022, background): “A powerful approach for this purpose is protein–ligand blind docking, which identifies the binding regions of a protein, and simultaneously predicts the binding pose of a molecule (3,4).”
• Toward prediction of functional protein pockets using blind docking and pocket search algorithms (2011, methodology): “The most important part of our test set was composed of 10 protein targets which had been found problematic in previous studies 7,8 using BD driven by AutoDock3.”
• Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors (2011, background): “Other methods dedicated to peptide docking have recently been developed but seem to be rather local as well [30,31,32], or restricted to very short peptides [33,34].”