Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only
Online Services

I-TASSER I-TASSER-MTD C-I-TASSER CR-I-TASSER QUARK C-QUARK LOMETS MUSTER CEthreader SEGMER DeepFold DeepFoldRNA FoldDesign COFACTOR COACH MetaGO TripletGO IonCom FG-MD ModRefiner REMO DEMO DEMO-EM SPRING COTH Threpp PEPPI BSpred ANGLOR EDock BSP-SLIM SAXSTER FUpred ThreaDom ThreaDomEx EvoDesign BindProf BindProfX SSIPe GPCR-I-TASSER MAGELLAN ResQ STRUM DAMpred

TM-score TM-align US-align MM-align RNA-align NW-align LS-align EDTSurf MVP MVP-Fit SPICKER HAAD PSSpred 3DRobot MR-REX I-TASSER-MR SVMSEQ NeBcon ResPRE TripletRes DeepPotential WDL-RF ATPbind DockRMSD DeepMSA FASPR EM-Refiner GPU-I-TASSER

BioLiP E. coli GLASS GPCR-HGmod GPCR-RD GPCR-EXP Tara-3D TM-fold DECOYS POTENTIAL RW/RWplus EvoEF HPSF THE-DB ADDRESS Alpaca-Antibody CASP7 CASP8 CASP9 CASP10 CASP11 CASP12 CASP13 CASP14

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. 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. Journal of Molecular Biology (2019) 431(13):2467-2476
  2. Yang Zhang, Jeffrey Skolnick (2005). TM-align: A protein structure alignment algorithm based on TM-score. Nucleic Acids Research, 33:2302-2309.
  3. Yang Zhang, Jeffrey Skolnick (2004). SPICKER: Approach to clustering protein structures for near-native model selection. Journal of Computational Chemistry, 25:865-871.
  4. 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.
  5. 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.

Back to EvoDesign Homepage

zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417