concanavalin-a and acadesine

Seven docking predictions were made with the LIGIN program. In six cases the location of the binding pocket was identified correctly by systematically docking everywhere within the protein structure. In two cases the ligand was docked to within 1.8 A RMSD of the experimentally determined structure. LIGIN has not been optimized to deal with highly flexible ligands that dock at the surface of proteins. Consequently, in three cases the exposed part of the ligand was docked poorly, although the buried parts were docked well, and made similar atomic contacts with the protein as in the experimentally determined structure.

Topics: Amiloride; Aminoimidazole Carboxamide; Arabinose; Concanavalin A; Enzyme Inhibitors; Fructose-Bisphosphatase; Humans; Ligands; Molecular Structure; Pancreatic Elastase; Pentamidine; Protein Conformation; Proteins; Ribonucleosides; Software; Trypsin

We have applied our docking program FlexX to all eight CASP2 targets involving protein complexes with small ligands. Of the seven targets that were kept in the CASP2 experiment, we could solve two. We found important parts of the solution in four other examples, and were unsuccessful on the remaining example. This paper discusses all predictions in detail. Each of our prediction runs took just a few minutes of computer time on a standard workstation and could thus be demonstrated in real time at the CASP meeting. We believe that this speed is the prime strength of our program FlexX. In quality, our predictions are competitive with those produced by other predictors. The experiment showed that possible objectives of improvement of the FlexX program are to incorporate relevant aspects of receptor flexibility, deal with water molecules in the receptor pocket, allow for a postoptimization to refine favorable complexes, and improve the scoring function.

Topics: Amiloride; Aminoimidazole Carboxamide; Arabinose; Concanavalin A; Fructose-Bisphosphatase; Ligands; Models, Molecular; Pancreatic Elastase; Pentamidine; Protein Conformation; Proteins; Ribonucleosides; Software; Trypsin