BioFET-SIM Web Interface: Implementation and Two Applications

Abstract

We present a web interface which allows us to conveniently set up calculations based on the BioFET-SIM model. With the interface, the signal of a BioFET sensor can be calculated depending on its parameters, as well as the signal dependence on pH. As an illustration, two case studies are presented. In the first case, a generic peptide with opposite charges on both ends is inverted in orientation on a semiconducting nanowire surface leading to a corresponding change in sign of the computed sensitivity of the device. In the second case, the binding of an antibody/antigen complex on the nanowire surface is studied in terms of orientation and analyte/nanowire surface distance. We demonstrate how the BioFET-SIM web interface can aid in the understanding of experimental data and postulate alternative ways of antibody/antigen orientation on the nanowire surface.

a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement

“…Once the working pH is assigned, the p K a Calc is obtained using the PROPKA software which also determines the burying percentage . A preliminary preparation of the PDB ( i ) ARM file, consisting of completing the heavy missing atoms of chain residues (including hydrogen atoms), is needed to guarantee the correct operation of PROPKA . This requires using the PDB2PQR , software, which operates under the following workflow: (i) check for missing heavy atoms, (ii) reconstruct heavy atoms, (iii) build and optimize hydrogens, and (iv) assign atomic parameters (for further details see ref ).…”

“…ARM file, consisting of completing the heavy missing atoms of chain residues (including hydrogen atoms), is needed to guarantee the correct operation of PROPKA. 77 This requires using the PDB2PQR 78,79 software, which operates under the following workflow: (i) check for missing heavy atoms, (ii) reconstruct heavy atoms, (iii) build and optimize hydrogens, and (iv) assign atomic parameters (for further details see ref 78). PDB2PQR is automatically launched using as input the PDB (i)…”

On the Physical Design of Molecular Communication Receiver Based on Nanoscale Biosensors

“…For example, the default value of ionic concentration, c ion , is selected according to the reported value for bovine serum (70mM) [46]; but in the sensitivity and SNR analyses, we investigate the performance for ionic concentrations corresponding to a wide range of solutions including highly diluted solutions (c ion =1mM) and human blood plasma (c ion >100mM) [47]. The solvent is water by default in physiological conditions, which implies the relative permittivity, R / 0 = 78 [48]. The employed receptors on the FET surface are considered to be aptamers, the production process of which provides full control over the selection of length, binding and unbinding rates, as well as the type of corresponding ligand molecules (see Section V-B).…”

“…The models used in the simulators assume ideal MC receivers with perfect sampling of concentration. On the other hand, bioFET simulators are developed mainly for the purpose of proper evaluation and classification of experimental results [48]. These frameworks lack underlying analytical models, thus, are not able to provide the required design and optimization tools.…”

Web-ARM: A Web-Based Interface for the Automatic Construction of QM/MM Models of Rhodopsins

“…Following the general interest in accessing complex computational chemistry tools through the web, − here we report on the design, implementation, and testing of Web-ARM, a web-accessible interface () built upon a -ARM and intended as a user-friendly and fast (with respect to the command-line version) builder of congruous and reproducible gas-phase QM/MM models (i.e., a -ARM models, see also section S1 in the Supporting Information for a description of the term gas-phase) of rhodopsins. Briefly, such gas-phase model refer to a globally uncharged trans-membrane protein where external Cl – and/or Na + counterions are properly placed in both the intracellular (IS) and extracellular (OS) protein surfaces to approximately mimic the effect of the water-solvation on the internal chromophore.…”