DeepHomo2.0 Server
[Huang Lab]   [DeepHomo2.0]   [Help]   [Output example]  
Protein Monomer Input using ONE of the following two options: [help]
  • Upload your pdb file in PDB format: [example]
    • OR copy and paste your pdb file below in plain text:                  (Sample input)

    Note: The monomer should contain no more than 1000 residues.
Options :
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Download the DeepHomo2.0 package new

References:
  1. Peicong Lin, Yumeng Yan, Sheng-You Huang, Improved protein-protein interaction prediction of homo-oligomeric complexes by Transformer-enhanced deep learning, Briefings in Bioinformatics, 2022 (in press).
In addition, users may also want to cite:
  1. Remmert M, Biegert A, Hauser A, Söding J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods. 2011 Dec 25;9(2):173-5.
  2. Seemayer S, Gruber M, Söding J. CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations. Bioinformatics. 2014;30(21):3128-30.
  3. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983;22(12):2577-2637.
  4. Yan Y, Huang SY. CHDOCK: a hierarchical docking approach for modeling Cn symmetric homo-oligomeric complexes. Biophys. Rep. 2019;5(2):65-72.
  5. Yan Y, Tao H, Huang SY. HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry. Nucleic Acids Res. 2018;46(W1):W423-W431.
  6. Wang S, Sun S, Li Z, Zhang R, Xu J. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. PLoS Comput Biol. 2017;13(1):e1005324.
  7. Rao R, Liu J, Verkuil R, et al. MSA Transformer. bioRxiv 2021.02.12.430858, 2021.
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