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Probe Development Tools Available from RECCR Curt Breneman April 30, 2007

Probe Development Tools Available from RECCR Curt Breneman April 30, 2007. Alignment-free Molecular Property Descriptors. Creation of Generic Data Mining Tools. pH 4 Mol 1 Mol 2 Mol 3 Mol 4 Mol 5 Mol 6 Mol 7 Mol 8 Mol 9 Mol 10 Mol 11 Mol 12 Mol 13 Mol 14. pH 5 Mol 1 Mol 2

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Probe Development Tools Available from RECCR Curt Breneman April 30, 2007

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  1. Probe Development Tools Available from RECCR Curt Breneman April 30, 2007

  2. Alignment-free Molecular Property Descriptors Creation of Generic Data Mining Tools pH 4 Mol 1 Mol 2 Mol 3 Mol 4 Mol 5 Mol 6 Mol 7 Mol 8 Mol 9 Mol 10 Mol 11 Mol 12 Mol 13 Mol 14 pH 5 Mol 1 Mol 2 Mol 3 Mol 4 Mol 5 Mol 6 Mol 7 Mol 8 Mol 9 Mol 10 Mol 11 Mol 12 Mol 13 Mol 14 Mol 15 Mol 16 Mol 17 pH 6 Mol 1 Mol 2 Mol 3 Mol 4 Mol 5 Mol 6 Mol 7 Mol 8 Mol 9 Mol 10 Mol 11 Mol 12 Mol 13 Mol 14 Mol 15 Mol 16 Mol 17 pH 7 Mol 1 Mol 2 Mol 3 Mol 4 Mol 5 Mol 6 Mol 7 Mol 8 Mol 9 Mol 10 Mol 11 Mol 12 Mol 13 Mol 14 Mol 15 pH 8 Mol 1 Mol 2 Mol 3 Mol 4 Mol 5 Mol 6 Mol 7 Mol 8 Mol 9 Mol 10 Mol 11 Mol 12 Mol 13 Mol 14 Multi-Objective Learning Non-linear Model Building and Validation Methods RECCR – Probe Development and Data Analysis Methods

  3. 1POC EP pH 3.0 1POC EP pH 4.0 1POC EP pH 5.0 1POC EP pH 6.0 1POC EP pH 7.0 1POC EP pH 8.0 1POC (Bee-venom Phospholipase A2 ) pH Sensitive EP Encoding by Matt Sundling

  4. Protein Structure “Cleaning” and Data Preparation Tool Select PDB structure from protein databank with the highest resolution and fewest number of missing amino acids. 1POC All PDBs have missing atoms, and many have missing amino acids 1POC - Bee-venom Phospholipase A2 Compute solvent accessible surface Remove water and heteroatoms Use clean PDB structure and protein sequence to form a homology model of the complete protein structure Encode with pH sensitive properties Now available on the RECCR website:http://reccr.chem.rpi.edu MOE descriptors pH independent Surface + charge descriptors pH dependent properties

  5. Protein Cleaner Interface

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