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EvoDesign Logo

EvoDesign is an evolution-based approach to de novo protein fold and protein-protein interaction design. 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 starting 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.

  EvoDesign Overview

  Submitting an EvoDesign Job

  Understanding the Output of EvoDesign

   Summary of Input

   Profile Information

   Design Clustering

   Design Summary Table

   Designed Sequences

   I-TASSER Modeling


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, Xiaoqiang Huang, Dani Setiawan, Yang Zhang. EvoDesign: Designing Protein-Protein Binding Interactions Using Evolutionary Interface Profiles in Conjunction with an Optimized Physical Energy Function. J Mol Biol (2019) S0022-2836(19)30118-4

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