CASP2 experiences with docking flexible ligands using FlexX.
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.
Kramer
B
B
German National Research Center for Information Technology (GMD), Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Germany. bernd.kramer@gmd.de
Rarey
M
M
Lengauer
T
T
D000584:Amiloride / Q000737:chemistry / Q000378:metabolism; D000620:Aminoimidazole Carboxamide / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D001089:Arabinose / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D003208:Concanavalin A / Q000737:chemistry / Q000378:metabolism; D006597:Fructose-Bisphosphatase / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D010196:Pancreatic Elastase / Q000737:chemistry / Q000378:metabolism; D010419:Pentamidine / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012263:Ribonucleosides / Q000737:chemistry / Q000378:metabolism; D012984:Software; D014357:Trypsin / Q000737:chemistry / Q000378:metabolism
D008024:Ligands; D011506:Proteins; D012263:Ribonucleosides; D003208:Concanavalin A; D000620:Aminoimidazole Carboxamide; C011651:acadesine; D010419:Pentamidine; D000584:Amiloride; D001089:Arabinose; D006597:Fructose-Bisphosphatase; D010196:Pancreatic Elastase; D014357:Trypsin