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):
yangzhanglabumich.edu | (734) 647-1549 | 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218