Database screening

TJA Ewing, ID Kuntz. Critical evaluation of search algorithms for automated molecular docking and database screening. J Comput Chem 18 1175-1189, 1997. 

Rastelli G, Ferrari AM, Constantino L, Gamberini MC. Discovery of new inhibitors of aldose reductase from molecular docking and database screening. Bioorg Med Chem 2002 10 1437-50. 

Rastelli G, Pacchioni S, Sirawaraporn W, Sirawaraporn R, Parenti MD, Ferrari AM. Docking and database screening reveal new classes of Plasmodium falciparum dihydrofolate reductase inhibitors. J Med Chem 2003 46 2834-45. 

Stahl, M. and Schulz-Gasch, T. Practical database screening with docking tools. In Small Molecule-Protein Interaction, Waldmann, H. and Koppitz, M. (Eds.). Springer-Verlag, Berlin and Heidelberg, 2003, 127-150. 

Su, A. I., Lorber, D. M., Weston, G. S., Baase, W. A., Mathews, B. W., and Shoichet, B. K. (2001) Docking molecules by families to increase the diversity of hits in database screens computational strategy and experimental evaluation. Proteins Struc. Func. Genet. 42, 279-293. 

In a growing number of studies, correlation-vector representations of pharmaco-phoric features of molecules have been proven to be useful in similarity searching and de novo design projects. They allow for rapid database screening, which... 

Chang C, Ekins S, Swaan P (2005) Application of P-gp pharmacophore models in database screening. In 229th ACS National Meeting, San Diego, p. 509. 

Nine strategies consistently appear in LC/MS-based methods for accelerated development (Table 5.1). The nine strategies are standard methods, template structure identification, databases, screening, integration, miniaturization, parallel processing, visualization, and... 

Figure 2.150. Ligprep is used for the rapid conversion of 2D structure files into accurate 3D models suitable for use in database screens and other applications. At the user s discretion Ligprep can generate multiple protonation states, enumerate chiralities, and generate tautomeric forms of the ligand...

Halgren TA, Murphy RB, Friesner RA et al (2004) Glide a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47(7) 1750-1759... 

PHASE a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening 1. Methodology and preliminary results. J Comput Aided Mol Des 20(10) 647-671... 

Good AC, Ewing TJ, Gschwend DA, Knntz ID (1995) New molecular shape descriptors application in database screening. J Comput Aided Mol Des 9 1-12... 

Search Algorithms for Automated Molecular Docking and Database Screening. 

Discovery of Novel Matriptase Inhibitors through Structure-Based 3D Database Screening, 269... 

After this general preselection, it can be advantageous to apply further steps of hierarchical filtering. As mentioned above, this could involve the selection of functional groups inevitably required to anchor a ligand to the most prominent interaction sites. Subsequently, the information of the "hot spot" analysis—translated into a pharmacophore hypothesis—can be used as matching criterion for a fast database screen. Such tools either involve fast tweak searching (355)or scan over precalculated conformers of the candidate molecules (356). The list of prospective... 

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