Ligand-protein cross-docking with water molecules.
The accuracy of ligand-protein docking may be affected by the presence of water molecules on the surface of the protein. Cross-docking simulations have been performed on a number of ligand-protein complexes for various proteins whose crystal structures contain water molecules in their binding sites. Only common sets of water molecules found in the binding site of the proteins were considered. A statistically significant overall increase in accuracy was observed when water molecules were included in cross-docking simulations. These results confirm the importance of including water molecules whenever possible in ligand-protein docking simulations.
Thilagavathi
Ramasamy
R
Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Pharmacy and Biomedical Sciences, Curtin University of Technology, Perth, WA 6845, Australia.
Mancera
Ricardo L
RL
D019747:Aldose-Ketose Isomerases / Q000737:chemistry / Q000378:metabolism; D000818:Animals; D001665:Binding Sites; D018360:Crystallography, X-Ray; D050556:Fatty Acid-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry / Q000378:metabolism; D017686:Oncorhynchus mykiss / Q000378:metabolism; D010407:Penicillium / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D011505:Protein-Tyrosine Kinases / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D051381:Rats; D012083:Renin / Q000737:chemistry / Q000378:metabolism; D013302:Streptomyces / Q000201:enzymology; D014867:Water / Q000737:chemistry / Q000378:metabolism*
D050556:Fatty Acid-Binding Proteins; D005656:Fungal Proteins; D008024:Ligands; D011506:Proteins; D014867:Water; D011505:Protein-Tyrosine Kinases; D009113:Muramidase; D012083:Renin; D019747:Aldose-Ketose Isomerases; C023298:xylose isomerase