Efficient Unbound Docking of Rigid Molecules

By Dina Schneidman-Duhovny, Ruth Nussinov, Haim J. Wolfson. Workshop on Algorithms in Bioinformatics, 2002

754 citations recorded by the source corpus.

Subfields: Biophysics, Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/45914901c0529f762f813213abb9f4e0874e3ddb

How researchers see this paper

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

In Biophysics

1. David Baker
2. Bruno E. Correia
3. Freyr Sverrisson
4. B. Coventry
5. Haim J. Wolfson
6. Ruth Nussinov
7. Nelly Andrusier
8. Sergey Ovchinnikov

In Computational Theory and Mathematics

1. David Baker
2. D. Ritchie
3. Iain H. Moal
4. Bruno E. Correia
5. Juan Fernández-Recio
6. Freyr Sverrisson
7. B. Coventry
8. Haim J. Wolfson

In Molecular Biology

1. David Baker
2. Sergey Ovchinnikov
3. D. Ritchie
4. Bruno E. Correia
5. Yang Zhang
6. Haim J. Wolfson
7. Juan Fernández-Recio
8. Ruth Nussinov

Citations in the corpus

• Antibody i-Patch prediction of the antibody binding site improves rigid local antibody-antigen docking. (2013, methodology): “In the manuscript, the results are shown for ZDOCK (PatchDock results which are similar are given in the Supplementary Information).”
• Computational design of environmental sensors for the potent opioid fentanyl (2017, methodology): “, 2005) using the fast docking algorithm PatchDock, which identifies shape complementary interactions between binding partners (Duhovny et al., 2002).”
• Principles of Flexible Protein-Protein Docking (2008, neutral): “77 Then, an assembly graph is constructed.”
• FireDock: Fast interaction refinement in molecular docking (2007, methodology): “4 Each candidate is subsequently refined by restricted interface side-chain rearrangement and by soft rigid-body optimization.”
• Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information (2014, methodology): “0, with clustering parameters (rmsd 0.5; discardClustersSmaller 0) ( Duhovny et al., 2002 ) to generate an ensemble of conformations that were then scored using all the restraints.”
• Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds (2020, methodology): “40 mini-proteins of mixed alpha/beta and all alpha topology were docked against barnase (PDB: 1BRS) using PatchDock[12,13] and the top 10 docks for each selected.”
• PatchDock and SymmDock: servers for rigid and symmetric docking (2005, methodology): “PatchDock (20) is a geometry-based molecular docking algorithm.”
• P HYSICS - INFORMED DEEP NEURAL NETWORK FOR RIGID - BODY PROTEIN DOCKING (2022, methodology): “PatchDock is a good baseline for a few different reasons: 1) Like our method it does not allow for intra-molecular flexibility, and only does rigid-body docking.”
• HexServer: an FFT-based protein docking server powered by graphics processors (2010, methodology): “These range from the rapid PatchDock server (3), which is based on a rigid-body geometric hashing algorithm (4), to much more computationally intensive approaches incorporating models of flexibility such as RosettaDock (5) and Haddock (6).”
• The scoring of poses in protein-protein docking: current capabilities and future directions (2013, methodology): “These range from composite scoring functions using a linear combination of terms, usually models of the underlying physical phenomena at play [52-65], to methods derived from the statistics of structural databases [63,66-70], docking decoys [71-75], experimental binding energies [76], methods based ”