For a given amino acid variation, PolyPhen performs several steps: (a) extraction of sequence-based features of the substitution site from the UniProt database, (b) calculation of profile scores for two amino acid variants, (c) calculation of structural parameters and contacts of a substituted residue.
Available analytical methods for the calculation of these profiles are evaluated and a numerical framework for the rigorous calculation has been developed.
A 3D structure was reconstructed and used for the calculation of flow profiles within the monolith and for calculation of pressure drop and permeability by computational fluid dynamics (CFD).
The axial velocity is expanded in terms of tangential harmonics, a technique that can be used in other geometries and lends itself to a relatively simple numerical calculation of velocity profiles in terms of the Dean number (De) and the curvature ratio.
The key mechanical properties of wellbore wall rock for calculation of stress profiles based on the uniaxial strain theory, such as Poisson's ratio, overburden and pore pressure, can be determined using acoustic logs including compressional and shear wave velocities together with density log.
The most time consuming is the estimation of the binding free energy, which for large interfaces and protein complexes requires intensive and long computational times, and the sequence search and calculation of sequence profiles for evolutionary-based measures.
A data-mining algorithm is developed and applied, which leads to the in silico calculation of "inflammation profiles" that highlight leukocyte subsets best able to explain gene expression patterns associated with high fat diet.
In all cases, the sample in question was excluded from the calculation of average profiles.
Furthermore, the 90 items of the inventory constitute three composite scores and nine symptom scales (Somatisation, Obsessive-Compulsive, Interpersonal Sensitivity, Depression, Anxiety, Hostility, Phobic Anxiety, Paranoid Ideation, Psychoticism) allowing the calculation of psychopathological profiles.
To eliminate biases due to recent gene expansions or alternatively spliced transcripts in the genomewide calculation of RSCU profiles, we clustered all transcripts with ≥ 80% sequence identity using cd-hit-est [ 32] (version 4.3 with -c 0.8 options).
