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BindProfX is a renewed approach to assess protein-protein binding free-energy changes (ΔΔG) induced by single- and multiple-mutations. This is an update on the BindProf method, which was designed to calculate the protein binding free-energy from the multiple sequence alignments of interface structure profiles. The major difference between BindProf and BindProfX is at the core algorithm to assess binding free-energy: While BindProf is based on the log-odds likelihood calculation, BindProfX calculates the binding free-energy change as the logarithm of relative probability of mutant amino acids over wild-type ones, which significantly increased the correlation to the experimental ΔΔG measurements. The improvement is mainly due to the introduction of multiple pseudo counts that account for the inter-amino acid mutation probability and improve the robustness of the profile score on limited structural library. BindProfX is particularly useful for designing and engineering protein-protein interactions with enhanced binding affinity. It has also the power to help understand roles of disease-related mutations associated with protein-protein interactions (>> Read more about BindProfX).

BindProfX Online (View an example of BindProfX server output)

From May. 10 to Jul. 30, 2020 (CASP14 season), the BindProfX server will be closed to external users. Please use the standalone version during this period. Jobs already submitted will not be affected. We apologize for any inconvenience this may cause.

  • Structure of Query Proteins in PDB format (Only dimer is considered.)
  • Specify mutations (Only mutation at the interface is considered.)
  • Your email address: (where results will be sent to)
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  • BindProfX Download

  • Download BindProfX standalone program and library.
  • Download BindProfX benchmark datasets.



    Reference:
    • Peng Xiong, Chengxin Zhang, Wei Zheng, Yang Zhang. BindProfX: Assessing mutation-induced binding affinity change by protein interface profiles with pseudo counts. J Mol Biol. 429: 426-434, 2017. [PDF] [Supplementary Information]
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