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... ligands (benzene, pyrrole derivatives). Tests the performance of DOCK in reproducing the poses of fragments; most programs should reproduce these systems with a high degree of success. This family was used as a model for FEP binding energy predictions (Mobley, Shoichet, Dill 2007) as the ligands are small and differ in minor sidechains. Streptavidin has biotin as the natural substrate, extremely high binding affinity. All ligands in this family are biotin and synthetic analogs. Ribonuclease T1 binds nucleotide ligands, with a charged binding site. High success rates 100%, 85.7% and 85.7% are seen, in addition to perfect sampling. There is a calcium ion in the binding site. These ligands are quite flexible with average of 13 rotatable bonds, and we dock then in with 100% success rigidly and fad, with flex docking limited by correct sampling in 4 of the six complexes.
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