ArticleProteins2017
New additions to the ClusPro server motivated by CAPRI.
Article in Proteins, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 321 papers.
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Who cites it
321 citing papers in PubMed.
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- Design of a global population-covering multi-epitope mRNA vaccine against Lassa virus using immunoinformatics.Scientific reports · 2026Article
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- Schistosome esophageal gland factor MEG-8.2 drives host cell lysis and interacts with host immune proteins.PLoS pathogens · 2026Article
- Design of a multiepitope immunotherapy for fish allergy.Scientific reports · 2026Article
- Computational design of a novel multi-epitope vaccine candidate against group A rotavirus.Virology journal · 2026Article
- Arginine 11, Arginine 32, and Lysine 44 of a Staphylococcal Anti-sigma Factor are Indispensable Residues.The protein journal · 2026Article
- Design and computational evaluation of a prophylactic and therapeutic multi-epitope vaccine candidate against cervical cancer.Virology journal · 2026Article
- Iron Regulatory Mechanism IRE/IRP-like in Two Protozoa of Importance to Human Health,Pathogens (Basel, Switzerland) · 2026Review
- Radiotherapy induces YTHDF2 in dendritic cells impairing cross-presentation and T cell function.The Journal of experimental medicine · 2026Article
- In Silico Identification of Antiviral Peptides as Potential Leads Against Sudan Ebolavirus VP-40.BioMed research international · 2026Article
261 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
The heavily used protein-protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for small angle X-ray scattering data in docking; (2) considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers. In addition, we have developed an extremely fast docking algorithm based on 5D rotational manifold FFT, and an algorithm for docking flexible peptides that include known sequence motifs. We feel that these developments will further improve the utility of ClusPro. However, CAPRI emphasized several shortcomings of the current server, including the problem of selecting the right energy parameters among the five options provided, and the problem of selecting the best models among the 10 generated for each parameter set. In addition, results convinced us that further development is needed for docking homology models. Finally, we discuss the difficulties we have encountered when attempting to develop a refinement algorithm that would be computationally efficient enough for inclusion in a heavily used server. Proteins 2017; 85:435-444. © 2016 Wiley Periodicals, Inc.
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