Blind Docking

Hetenyi C, van der Spoel D (2006) Blind docking of drug-sized compounds to proteins with up to a thousand residues. FEBS Lett 580 1447-1450... 

Grosdidier, A., Zoete, V., and Michielin, O. (2009) Blind docking of 260 protein-ligand complexes with EADock 2.0. Journal of Computational Chemistry, 30, 2021-2030. 

Monte Carlo simulations [15]. The concept of hotspot permitted a straightforward distribution on a grid. In fact, each hotspot can be computed on a different node of the grid. To run a full blind docking calculation, it is necessary to send three files to the Master the receptor and the ligand in pdbqt format, and a text file containing the conservation string. An example of the text file is ... 

Ghersi D, Sanchez R(2009) Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites. Proteins 74 417-24... 

Performing a validated blind prediction is a difficult task and requires the availability of the software, a test scenario, and the experimental facilities for validating the study. For protein-protein docking, a blind prediction of the complex between TEM-1 /Mactamase and the inhibitor BLIP was performed by 6 independent groups. All groups were able to identify the correct complex within 2 A RMSD [153]. 

We will then survey several alternative approaches for protein-protein docking. A true test of any predictive method is its success in blind trials since this prevents bias for over optimisation during the development of the approach. There have been two such blind trials and the results will be described. In addition to this chapter, the reader is referred to other reviews of the field [7-9]. 

From only two blind trials, one cannot draw definitive conclusions. However, in both challenges the Fourier correlation approach of Katchalski-Katzir yielded the best submission which suggests that it must be considered as a valuable strategy for macromolecular docking. 

Damm-Ganamet KL, Smith RD, Dunbar JB, Stuckey JA, Carlson HA (2013) CSAR benchmark exercise 2011-2012 evaluation of results from docking and relative ranking of blinded congeneric series. J Chem Inf Model. doi 10.1021/ci400025f... 

M. F. Lensink and S.J. Wodak, Profei s, 78,3085-3095 (2010). Blind Predictionsof Protein Interfaces by Docking Calculations in CAPRI. 

R. Mendez, R. Leplae, L. De Maria, and S. J. Wodak, Proteins, 52, 51-67 (2003). Assessment of Blind Predictions of Protein-Protein Interactions Current Status of Docking Methods. 

Mirrors on the lift truck as well as those mounted at blind corners, walkways, and dock areas are necessary. Also, any areas where red or yellow flashing lights could be mounted will warn the pedestrian of an approaching lift truck. These should be used where visibility is limited and pedestrian safety requires visual and audible warnings. Even the horn of the forklift can provide a warning to those on foot. 

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