Bioinformatics, Protein electrostatics, NMR, Image processing (microarrays processing, AFM image analyses, ...), time resolved fluorescence streak data processing, pump probe data (transient absorption) processing,

The TITRA program, is a protein titration program implementing the Tanford-Kirkwood (TK) sphere model for site-site interactions (see Figure 4-8 of attched paper) (Tanford and Kirkwood, 1957; Martel, 1996) and the Tanford-Roxby iterative mean field approximation (Tanford and Roxby, 1972) for calculation of the average protonation state of the titratable sites. Here we will outline the general workings of the program. The general flow of the TITRA program is shown in the figure below. First, files containing atomic (AA) or solvent (SA) exposed area of individual atoms, pK^int for each of the titratable sites and Tanford-Kirkwood model parameters are read, and user options and arguments processed. A set of titratable residues and atomic locations for charge placement are selected according to default internal rules and/or information specified in user input files.

Values for the site-site coupling function W_ij (described in the paper attached) are then computed, using the Tanford-Kirkwood formula (equation 4.68 of the attached paper), for a range of distances specified by the cut-off values, and stored in a table for later use. The fractional charge of each site is computed at the starting pH value, using the pK^int value for that group and equation 4.50 (see attched paper). The total electrostatic potential at each group, generated by the remaining groups, is determined using the previously calculated partial charges and W_ij coupling terms, which may be adjusted by the Modified Tanford-Kirkwood correction factor (1-SA_ij) (Shire et al., 1974), depending on the user input options. The total potential at the site is then used to calculate its DpK^eff value, and the site pK^eff is updated. After all site pK^eff values have been updated, a new circle starts. Iteration proceeds until the change in calculated mean charges z_i and pK^eff values goes below a predefined error tolerance or the maximum allowed number of iterations is reached. The whole iterative procedure is repeated for the range of pH values requested by the user, and the total charge and pK^eff values at each pH are stored in separate output files.

Special Modules for:

This module allows for a complete analysis of the optical recording of the biosensor array. In addition to analyzing the array in terms of individual spot parameters, it allows the user to pick the optimal parameter for further study of his data. More than 10 such measurable parameters are computed by the SW. In addition, it will assess the quality and precision of the spotting technology used. The most important feature of the SW is that it can compute that certainty for a diagnostic outcome, based on the micro array response to a given biomarker.

See explanatory presentations on how data can be analysed:

-BNIP Pro presentation 1

-BNIP Pro presentation 2

Micro Array Images are often of poor intensity and pose great demands on baseline correction routines. The BNIP array processing module provide the user with a range of powerfull tools for analyzing micro array images.

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