The ClusPro web server for protein-protein docking

By Dima Kozakov, David R. Hall, Bing Xia, Kathryn A. Porter, D. Padhorny, Christine Yueh, Dmitri Beglov, Sandor Vajda. Nature Protocols, 2017

2,958 citations recorded by the source corpus.

The ClusPro server (https://cluspro.org) is a widely used tool for protein–protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.

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Citations in the corpus

• Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets (2017, methodology): “Table 2 summarizes recent published results from five leading docking methods: HADDOCK (Vangone et al. , 2017), iATTRACT (Schindler et al. , 2015), ClusPro (Kozakov et al. , 2017), ZDOCK (Pierce et al. , 2011) and RosettaDock 3.2 (Chaudhury et al. , 2011).”
• Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. (2020, unknown): “Docking models were produced using ClusPro ( 81 ), ZDock ( 82 ), HDock ( 83 ), Gramm-X ( 84 ), SwarmDock ( 85 ), and PatchDock ( 86 ) with SOAP-PP score ( 87 ).”
• SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2 (2020, unknown): “php) (Kozakov et al., 2013; Kozakov et al., 2017; Vajda et al., 2017).”
• What Method to Use for Protein-Protein Docking? (2019, methodology): “We also tested our protein docking server ClusPro [24] by predicting the structures of the complexes added in Benchmark 5 [2].”
• InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs (2018, unknown): “For commercial re-use, please contact journals.permissions@oup.com cently moved to the ROSIE server (20)); docking with more than two proteins (ClusPro, GRAMM-X); and docking including degrees of flexibility (SwarmDock (21), ATTRACT (22), HADDOCK (23)).”
• Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking (2021, methodology): “…to improve PPIs from different aspects (Humphreys et al., 2021; Pei et al., 2021; Jovine), e.g., combining physics-based docking method C LUSPRO (Kozakov et al., 2017; Ghani et al., 2021), or using extended multiple-sequence alignments to predict the structure of heterodimeric protein complexes…”
• Automatic structure prediction of oligomeric assemblies using Robetta in CASP12 (2017, background): “…and oligomeric state assignment simultaneously; many efforts subdivide the problem into 2 tasks 1 : structure prediction, 2 – 5 which considers determination of the constituent monomers, and protein docking, 6 – 9 which considers predicting the structure of assemblies from largely rigid monomers.”
• The HDOCK server for integrated protein–protein docking (2020, background): “ClusPro is a cluster-based docking approach that may consider some entropic effects 38 .”
• HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA (2019, methodology): “According to the rules of CAPRI, the server groups must submit their results within 2 days, but the human predictor groups have ∼20 days and can use any additional information (6).”
• Performance and its limits in rigid body protein-protein docking (2020, unknown): “In the balanced set 00, the weighting coefficients are selected to yield similar weights for the four different energy terms (Kozakov et al., 2017).”