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EvoDesign Logo

EvoDesign is an evolution-based approach to de novo design of proteins and protein-protein interactions. It takes the full-atomic model of a scaffold in PDB format and outputs a list of designed sequences along with the percent sequence identity of each sequence to the scaffold. EvoDesign also provides normalized relative errors for predicted secondary structure, solvent accessibility, and backbone torsional angles with respect to the input. This helps the user understand the quality of the designed sequences.

  • Overview of EvoDesign
  • Making Input to EvoDesign
  • Understanding output of EvoDesign

  • References

    1. Yang Zhang, Jeffrey Skolnick (2005). TM-align: A protein structure alignment algorithm based on TM-score. Nucleic Acids Research, 33:2302-2309.
    2. Yang Zhang, Jeffrey Skolnick (2004). SPICKER: Approach to clustering protein structures for near-native model selection. Journal of Computational Chemistry, 25:865-871.
    3. Andrea Bazzoli, Andrea G. B. Tettamanzi, Yang Zhang (2011). Computational Protein Design and Large-Scale Assessment by I-TASSER Structure Assembly Simulations. Journal of Molecular Biology, 407:764-776.
    4. Pralay Mitra, David Shultis, Jeffrey R. Brender, Jeff Czajka, David Marsh, Felicia Gray, Tomasz Cierpicki, Yang Zhang (2013). An evolution-based approach for de novo protein design and a case study on Microbacterium tuberculosis. PLOS Computational Biology,9: e1003298.
    5. Robin Pearce, Dani Setiawan, Xiaoqiang Huang, Yang Zhang (2018). EvoDesign: Designing protein-protein binding interactions using evolutionary interface profiles, in preparation.
    6. Ambrish Roy, Alper Kucukural, Yang Zhang (2010). I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5:725-738.
    7. Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang (2015). The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8.

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