Protein–protein docking dealing with the unknown

By Irina S. Moreira, Pedro Alexandrino Fernandes, Maria João Ramos. 2009

130 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology, Computational Biology & Bioinformatics

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. Alexandre M. J. J. Bonvin
2. Brian G. Pierce
3. Yang Zhang
4. András Szilágyi
5. Anna Vangone
6. Zhiping Weng
7. João P. G. L. M. Rodrigues
8. M. V. van Dijk

In Materials Chemistry

1. András Szilágyi
2. Alexandre M. J. J. Bonvin
3. Yang Zhang
4. M. V. van Dijk
5. Brian G. Pierce
6. Zeynep Kurkcuoglu
7. João P. G. L. M. Rodrigues
8. Sjoerd Jacob de Vries

In Molecular Biology

1. Alexandre M. J. J. Bonvin
2. András Szilágyi
3. Brian G. Pierce
4. M. V. van Dijk
5. Yang Zhang
6. Zeynep Kurkcuoglu
7. João P. G. L. M. Rodrigues
8. Zhiping Weng

In Computational Biology & Bioinformatics

1. András Szilágyi
2. Zeynep Kurkcuoglu
3. M. V. van Dijk
4. Alexandre M. J. J. Bonvin
5. Zhiping Weng
6. João P. G. L. M. Rodrigues
7. Brian G. Pierce
8. Yang Zhang

Citations in the corpus

• Molecular Docking and Structure-Based Drug Design Strategies (2015, background): “Information provided by biomolecular NMR spectroscopy has been used to define PPI interfaces and determine the reciprocal orientation of the two binding partners [123].”
• The HADDOCK web server for data-driven biomolecular docking (2010, methodology): “HADDOCK has also performed very well in the CAPRI blind docking experiment (11 out of 15 complexes achieved the root mean square deviation (RMSD) 2 Å criterion for a CAPRI two-star evaluation) 6,7 and is currently the most cited biomolecular docking program 12 .”
• Template-based structure modeling of protein-protein interactions (2013, methodology): “The final model is selected from those with the best shape complementa rity, desolvation free energy and electrostatic matches between interfaces of the com ponent structures [9-12].”
• Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 (2017, background): “The success of HADDOCK in modeling protein–protein, protein-nucleic acid and protein–peptide complexes has been demonstrated numerous times (for a review, see [7]).”
• Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems (2019, background): “19 HADDOCK can handle mixed systems of proteins, nucleic acids and small molecules.”
• Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library (2011, background): “Molecular docking approaches, which take two (or more) structures as input and predict the structure of their complex, are increasingly being used for this purpose [2].”