pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking

By Tammy M. K. Cheng, Tom L. Blundell, Juan Fernández-Recio. Proteins: Structure, Function, and Bioinformatics, 2007

313 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/004af193841729539f38f9e83de160ba35b76e12

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. Shengyou Huang
2. Xiaoqin Zou
3. Juan Fernández-Recio
4. Iain H. Moal
5. Paul A. Bates
6. Mieczyslaw Torchala
7. Alexandre M. J. J. Bonvin
8. Brian G. Pierce

In Genetics

1. Shengyou Huang
2. Xiaoqin Zou
3. Paul A. Bates
4. Iain H. Moal
5. Mieczyslaw Torchala
6. Juan Fernández-Recio

In Molecular Biology

1. Shengyou Huang
2. Brian G. Pierce
3. Xiaoqin Zou
4. Alexandre M. J. J. Bonvin
5. Juan Fernández-Recio
6. Iain H. Moal
7. Paul A. Bates
8. Mieczyslaw Torchala

Citations in the corpus

• Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants (2021, background): “Developments such as explicit side chain flexibility during docking searches [8], use of normal mode analysis to represent protein flexibility [9, 10], clustering [11, 12] or re-scoring [13-16] docking models to improve ranking of near-native models, and use of experimental data as restraints for do”
• Contacts-based prediction of binding affinity in protein–protein complexes (2015, background): “…); data of the composite scoring ZRANK ( Pierce and Weng, 2007 ), ZRANK2 ( Pierce and Weng, 2008 ), RosettaDock ( Chaudhury et al., 2010 ), PyDock ( Cheng et al., 2007 ), FireDock (the total energy, the antibody–antigen energy and the enzyme-inhibitor energy) ( Andrusier et al., 2007 ), PISA (…”
• Updates to the integrated protein-protein interaction benchmarks: Docking benchmark version 5 and affinity benchmark version 2 (2015, methodology): “Properties of the non-interacting surface were found to correlate with affinity [13,27] and Δ Δ the PyDock [31], SIPPER [67], ZDOCK [68] and FireDock [69] docking scores, as well as contact potentials (ΔΔG_AW, ΔΔG_AU, ΔΔG_CW,”
• Performance and its limits in rigid body protein-protein docking (2020, unknown): “, 2003), GRAMM (Tovchigrechko and Vakser, 2005, 2006), pyDOCK (Cheng et al., 2007), and FTDock (Gabb et al.”
• The scoring of poses in protein-protein docking: current capabilities and future directions (2013, methodology): “PYDOCK_TOT [54] i The PyDock scoring function and the electrostatics, van der Waals and desolvation terms it is composed from.”
• An iterative knowledge‐based scoring function for protein–protein recognition (2008, methodology): “25,36,37 Because of is simplicity and fast speed, shape complementarity-based scoring methods are commonly used in the initial filtering stage of many docking programs such as ZDOCK and 3D-DOCK.”