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Internet Electronic Journal of Molecular Design - IEJMD, ISSN 1538-6414, CODEN IEJMAT
ABSTRACT - Internet Electron. J. Mol. Des. March 2005, Volume 4, Number 3, 194-209

New Application Design for a 3D Hydropathic Map-Based Search for Potential Water Molecules Bridging between Protein and Ligand
Glen E. Kellogg, Micaela Fornabaio, Deliang L. Chen, and Donald J. Abraham
Internet Electron. J. Mol. Des. 2005, 4, 194-209

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Abstract:
The design of an extension to the HINT (Hydropathic INTeractions) program for locating and automatically placing in relevant orientations bridging water molecules is described in detail. This application is used to analyze the structures of HIV-1 protease-inhibitor complexes for five key bridging water molecules. The tool locates the water molecules with an overall accuracy of 1.28 ± 0.55 Å, and orients them (relative to potentially erroneous molecular mechanics optimized water molecules) to 41 ± 23 degrees. This automated placement is in contrast to other programs that calculate 3D contour maps of energetically-likely binding locations for water molecules, which must be followed by manual placement and energy minimization of these water positions and orientations to create the model. Also, the new object-oriented toolkit design for the HINT program (http://www.edusoft-lc.com/toolkits/) is described. The toolkit includes molecule, atom and monomer objects to represent chemical structure. A second class of objects describes 3D maps and includes tools for their manipulation. The hint objects are designed around the primary goals of HINT: partitioning (calculating LogPo/w for) molecules, calculating interaction scores between molecules and calculating 3D maps of molecular and intermolecular hydropathy.

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