●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

EDock base on replica-exchange Monte Carlo simulations aims to high-quality blind docking built on low resolution protein structure prediction. Starting from a query protein sequence, I-TASSER is first used to predict 3D model of the target protein, where the ligand binding site can be predicted by COACH The initial ligand poses are generated by a modified graph matching on the predicted binding pockets. Replica-exange Monte Carlo (REMC) simulations are performed for ligand conformation sampling under the guidance of a physical force field coupled with binding site constraints, where the ligand docking model is finally selected by a composite knowledge-based score function.

The output of the EDock server include (Example output):

• Predicted binding sites by COACH.
• Docked poses by EDock simulation.

Input your receptor PDB structure from your computer:
(either structure in PDB format is acceptable or Example input )



Input your ligand MOL2 structure from your computer:
(either structure in MOL2 format is acceptable or Example input )



Email: (mandatory, where results will be sent to.)


Advanced options

• Receptor structure type:
  The input receptor structure is native 3D structure
  The input recetor structre is predicted 3D structure
• Whether predict binding sites by COACH
  Assign binding sites by COACH
  Specify binding sites by user Example input
  
  
  

• EDock standalone package
• EDock benchmark dataset collected from DUDE and COACH

• Wenyi Zhang, Eric Bell, Minghao Yin, Yang Zhang. EDock: Blind Protein-ligand Docking by Replica-Exchange Monte Carlo Simulation. Journal of Cheminformatics, 12: 37 (2020). [PDF] [Support Information]