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Table 3 Real running time T R of the IFACEwat in re-ranking some of the protein complexes and the estimated formula of the MD time for the structural refinement stage of the IFACEwat results as compared to ZDOCK

From: IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking

Complex Type IFACEwat re-ranking time T R (second/~minute) Expected MD refinement timeb to obtain at least 1 near native structure using
    ZDOCK IFACEwat
    Rank of 1st Hit MD time Rank of 1st Hit MD tìme
4CPA E 489.9/8.2 51 51 * TDi 4 4 * TDi
1QA9 O 542.9/9.1 2 2 * TDi 1 TDi
2AYO O 1109.8/18.5 32 32 * TDi 10 10 * TDi
2HLE O 819.0/13.6 2 2 * TDi 1 TDi
2VDB O 864.0/14.4 57 57 * TDi 18 18 * TDi
3BP8 O 500.8/8.3 11 11 * TDi 3 3 * TDi
1BGX A 1215.4/20.2 - 2000 * TDi 1 TDi
1KXQ AB 1289.5/21.5 - 2000 * TDi 1 TDi
2O3B E 632.4/10.5 7 7 * TDi 5 5 * TDi
1YVB E 855.5/14.2 - 2000 * TDi 2 2 * TDi
1FLE E 564.0/9.4 6 6 * TDi 4 4 * TDi
1AK4 O 290.4/4.8 - 2000 * TDi 3 3 * TDi
1H9D O 954.9/15.9 - 2000 * TDi 1 TDi
1HCF O 738.7/12.3 - 2000 * TDi 1 TDi
1RV6 O 848.2/14.1 - 2000 * TDi 3 3 * TDi
1Z0K O 859.6/14.3 - 2000 * TDi 1 TDi
2A9K O 678.9/11.3 - 2000 * TDi 2 2 * TDi
2BTF O 1130.1/18.8 6 6 * TDi 1 TDi
2OOR O 1297.8/21.6 - 2000 * TDi 1 TDi
  1. aRe-ranking of 2000 predictions of each protein complex on an Intel Xeon CPU E5540@2.53GHz machine. bAssume that each conformation of each complex takes equivalent time during the MD simulation, i.e. TDi. "-" means ZDOCK does not obtain any hit in the corresponding case
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