SCREEN

SCREEN2 is a tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis. SCREEN2 is an update on SCREEN.

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Description

Screen2 is a tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis. The original Screen, written by Murad Nayal, was dependent on the obsolete Irix platform and is no longer available. Screen2 was reengineered by Brian Y. Chen for efficiency and compatibility, and made accessible as a web service by Raquel Norel.

The primary difference between Screen and Screen2 is the update or replacement of several data gathering components. The most important component change replaces surface generation used in Screen with a higher resolution method for surface generation derived from Trollbase (written by Donald Petrey).As a result, geometric and electrostatic attributes are evaluated at a significantly larger number of individual points on the molecular surface. In principle, this higher resolution approach is more accurate, but because the underlying quantities now differ from Screen, the cavity attributes also now differ from Screen. Since the druggability index was computed with a classifier trained on the older attributes, the druggability index, as calculated on new attributes, differs, sometimes significantly, from values computed with Screen. For this reason, the druggability index is no longer supplied in the output. A detailed explanation of all cavity attributes is available: Definitions and List.

References

Nayal M, Honig B. On the nature of cavities on protein surfaces: application to the identification of drug binding sites. Proteins. 2006 Jun 1;63(4):892-906.

Acknowledgments

SCREEN was supported by a funding from the NSF Grant # DBI9904841. SCREEN2 is supported by a funding from the NIH Grant # GM030518.

Developed in the Honig Lab

Questions

For questions related to SCREEN, contact honig_software@c2b2.columbia.edu.