The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
FiberDock: Flexible induced‐fit backbone refinement in molecular docking
Open accessAbstract
Upon binding, proteins undergo conformational changes. These changes often prevent rigid‐body docking methods from predicting the 3D structure of a complex from the unbound conformations of its proteins. Handling protein backbone flexibility is a major challenge for docking methodologies, as backbone flexibility adds a huge number of degrees of freedom to the search space, and therefore considerably increases the running time of docking algorithms. Normal mode analysis permits description of protein flexibility as a linear combination of discrete movements (modes). Low‐frequency modes usually describe the large‐scale conformational changes of the protein. Therefore, many docking methods model backbone flexibility by using only few modes, which have the lowest frequencies. However, studies show that due to molecular interactions, many proteins also undergo local and small‐scale conformational changes, which are described by high‐frequency normal modes. Here we present a new method, FiberDock, for docking refinement which models backbone flexibility by an unlimited number of normal modes. The method iteratively minimizes the structure of the flexible protein along the most relevant modes. The relevance of a mode is calculated according to the correlation between the chemical forces, applied on each atom, and the translation vector of each atom, according to the normal mode. The results show that the method successfully models backbone movements that occur during molecular interactions and considerably improves the accuracy and the ranking of rigid‐docking models of protein–protein complexes. A web server for the FiberDock method is available at: http://bioinfo3d.cs.tau.ac.il/FiberDock. Proteins 2010. © 2009 Wiley‐Liss, Inc.
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Cites
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187
PatchDock and SymmDock: servers for rigid and symmetric docking
Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki481 · Cited by 3,018
Self-citationFolding funnels and binding mechanisms
Ma, B., Kumar, S., Tsai, C.-J., & Nussinov, R. (1999) · Protein Engineering, Design and Selection · doi:10.1093/protein/12.9.713 · Cited by 594
Self-citationMultiple diverse ligands binding at a single protein site: A matter of pre‐existing populations
Ma, B., Shatsky, M., Wolfson, H. J., & Nussinov, R. (2002) · Protein Science · doi:10.1110/ps.21302 · Cited by 420
Self-citationProgress in Modeling of Protein Structures and Interactions.
Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., & Baker, D. (2005) · Science · doi:10.1126/science.1112160 · Cited by 294 · cited 1×
“50,51 We used the 500 refined near-native complexes of FiberDock , FireDock, and RosettaDock , generated in the local docking experiments described earlier, to draw energy funnels around the native orientation of the ligands.”
MethodStructured disorder and conformational selection
Tsai, C., Ma, B., Sham, Y. Y., Kumar, S., & Nussinov, R. (2001) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.1107 · Cited by 202
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Tuncbag, N., Gursoy, A., Nussinov, R., & Keskin, O. (2011) · Nature Protocols · doi:10.1038/nprot.2011.367 · Cited by 263
Self-citationPRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes
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GTP-Dependent K-Ras Dimerization
Muratcioglu, S., Chavan, T. S., Freed, B. C., Jang, H., Khavrutskii, L., Freed, R. N., Dyba, M. A., Stefanisko, K., Tarasov, S. G., Gursoy, A., et al. (2015) · Structure · doi:10.1016/j.str.2015.04.019 · Cited by 202
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Kotev, M., Soliva, R., & Orozco, M. (2016) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2016.08.010 · Cited by 25
Developments in integrative modeling with dynamical interfaces
Ozdemir, E. S., Nussinov, R., Gursoy, A., & Keskin, O. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.10.007 · Cited by 17
Induced fit with replica exchange improves protein complex structure prediction
Harmalkar, A., Mahajan, S. P., & Gray, J. J. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010124 · Cited by 16
Main methods and tools for peptide development based on protein-protein interactions (PPIs)
Baeza, J., Bedoya, M., Cruz, P., Ojeda, P., Adasme-Carreño, F., Cerda, O., & González, W. (2025) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2025.151623 · Cited by 8
Metadata
- Authors
- Mashiach, E., Nussinov, R., & Wolfson, H. J.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2010-01-14
- Volume
- 78
- Issue
- 6
- Pages
- 1503-1519
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2090183113
- Cited by
- 187
- References
- 6
- FWCI
- 5.04
- Type
- journal article
- Language
- en
- Open access
- green
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