Detailed Discussion of Families Docking Results and Drugs. Essay

Detailed Discussion of Families Docking Results and Drugs. Essay

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Estrogen receptor regulates gene expression on binding the steroid hormone estradiol. Ligands in this family are typically large, rigid molecules 2-3 polar groups, and easy to dock to. Perfect sampling and high scoring success is observed in almost all the 47 complexes in this family. Complexes with the native substrate include estradiol 1QKT, 1QKU, 1A52. Trypsin is a serine protease found in the small intestine. It has a highly charged binding site with a triad of three catalytic residues His57, Asp102 and Ser195. There is a Calcium ion in the binding site. A large amount of crystallographic data is available for this protein, primarily because it is easily available and storable. Sampling (RGD=100%, FAD=89%, FLX=82.6%) and scoring (RGD=86.9%, FAD=73.9, FLX=54.3) drop gracefully. RGD sampling is perfect, but drops in FAD, FLX indicating trypsin ligands might benefit from a finer conformational sampling of the ligand torsions. Neuraminidase is the target for flu drugs, especially important with the threat of avian and swine flu. The natural substrate is neuraminic acid, a 9-carbon sugar molecule. This is a highly charged binding site, which responds well to docking efforts. Even though ligands have an average of 9 rotatable bonds, almost perfect sampling (95-98%) and scoring (93-86%) success is achieved. Since this is a tetramer with four non-interfacial binding sites, only the monomer was retained in this testset. Xtalmin scores clearly indicate the loss of binding in the mutants, WT = -72.6, while R292K = -68.9 and E119G=-68.1. The same ordering is captured in the scores of the top ranked poses for the flex docking results WT=-70.8, while R292K = -72.4 and E119G=-76.4, although the trend is not high enough to get ...

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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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