Protein interaction property similarity analysis

For proteins, a similarity analysis is typically most revealing for the MEP but can be computed for other MIFs. The MIF similarity analysis is implemented in PIPSA (Protein Interaction Property Similarity Analysis) [8, 47] (The PIPSA software can be obtained via http //projects.villa-bosch.de/mcm/). In the PIPSA pro-... 

R. C. Wade, R. R. Gabdoullme and F. De Rienzo, Protein Interaction Property Similarity Analysis, Int. J. Quantum Chem. 2001, 83, 122-127. 

In the case of E2 ubiquitin conjugating enzymes, the interaction properties of about 200 protein structures were compared [49]. The pairwise similarity matrix was visualized as a dendrogram and a kinemage projection to three-dimensional space (see www.ubiquitin-resource.org). The analysis revealed relations between functional groupings and electrostatic properties at specific parts of the protein structure. 

Similar to protein-DNA interactions, protein-RNA interactions also perform vital roles in the cell including protein synthesis, viral replication, cellular defense and developmental regulation [145,146]. One major direction in the analysis of protein-RNA interactions is to identify proteins that bind RNA based on features derived from physio-chemical properties of the sequence. A number of published works have focused casting this problem as a binary classification problem using the support vector machines (SVM) classifier to identify proteins that bind RNA [33-35, 51]. Each of these works derived large data sets from the SwissProt database and applied the support vector machines classifier to discriminate protein sequences that bind RNA from all other sequences. Since sequence analysis techniques can identity homologous proteins as having similar function, most of these works reduced the redundancy of the data sets below a certain threshold <40% [35], < 25%... 

Monolayers of micro- and nanoparticles at fluid/liquid interfaces can be described in a similar way as surfactants or polymers, easily studied via surface pressure/area isotherms. Such studies provide information on the properties of particles (dimensions, interfacial contact angles), the structure of interfacial layers, interactions between the particles as well as about relaxation processes within the layers. Such type of information is important for understanding how the particles stabilize (or destabilize) emulsions and foams. The performed analysis shows that for an adequate description of II-A dependencies for nanoparticle monolayers the significant difference in size of particles and solvent molecules has be taken into account. The corresponding equations can be obtained by using a thermodynamic model developed for two-dimensional solutions. The obtained equations provide a satisfactory agreement with experimental data of surface pressure isotherms in a wide range of particle sizes between 75 pm and 7.5 nm. Moreover, the model can predict the area per particle and per solvent molecule close to real values. Similar equations were applied also to protein monolayers at liquid interfaces. 

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