Alignment profile

If two or more types of amino acids are observed in an aligned profile defining position, P(Y Y) is first set to zero and the remaining I X Y)s prior conditional probabilities renormalized,... 

Wang N, DeLisle RK, Diller DJ. Fast small molecule similarity searching with multiple alignment profiles of molecules represented in one-dimension. J Med... 

Cuff, J. A. and G. J. Barton, Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins, 2000. 40(3) p. 502-11. 

With the growing number of proteins sequenced, there is a necessity for novel techniques to analyze protein sequences in order to determine their structure and function. The most commonly used protein sequence descriptors are based on evolutionary information and physicochemical properties. Even though these methods have proven to be efficient in most cases, in cases of transmembrane proteins, they may fall short. As the vast field of transmembrane proteins largely remains unexplored with many transmembrane proteins yet to be sequenced, it is possible to obtain new protein sequences without any known homolog. In such cases, traditional sequence analysis methods based on alignment profiles would not be sufficient. The evolutionary information-based descriptors appear inadequate, and indices based on physicochemical property can cause ambiguities. Therefore, it is of considerable interest to develop novel methods based on sequence information alone to represent protein sequences. 

More recently, the circular array was proposed to assess the reflectivity of cylindrical specimens [3]. First, a circular C-scan image was obtained. The total scan time was about 25 min., which does not include a relatively time consuming alignment of the specimen. From the circular C-scan image, circular B-scan profiles were chosen in specific planes. The transducer was a focused high frequency transducer with a center frequency of 25 MHz of the transducer bandwidth. This frequency corresponds to a wavelength of 0.11 mm and 0.25 mm in the Plexiglas specimen and the AlSi-alloy, respectively. Additional experimental parameters are presented in Table 1. 

To achieve the lowest possible delay a bipolar switching transistor developed by IBM minimizes parasitic resistances and capacitances. It consists of self-aligned emitter and base contacts, a thin intrinsic base with an optimized collector doping profile, and deep-trench isolation (36). Devices must be isolated from each other to prevent unwanted interactions in integrated circuits. While p—n junctions can be used for isolation, IBM s approach etches deep trenches in the siUcon wafer which are filled with Si02 to provide electrical insulation. 

Figure 12 ModBase, a database of comparative protein stracture models. Screenshots of the following ModBase panels are shown A form for searching for the models of a given protein, summary of the search results, summary of the models of a given protein, details about a single model, alignment on which a given model was based, 3D model displayed by RASMOL [237], and a model evaluation by the Prosall profile [217],...

A prior distribution for sequence profiles can be derived from mixtures of Dirichlet distributions [16,51-54]. The idea is simple Each position in a multiple alignment represents one of a limited number of possible distributions that reflect the important physical forces that determine protein structure and function. In certain core positions, we expect to get a distribution restricted to Val, He, Met, and Leu. Other core positions may include these amino acids plus the large hydrophobic aromatic amino acids Phe and Trp. There will also be positions that are completely conserved, including catalytic residues (often Lys, GIu, Asp, Arg, Ser, and other polar amino acids) and Gly and Pro residues that are important in achieving certain backbone conformations in coil regions. Cys residues that form disulfide bonds or coordinate metal ions are also usually well conserved. 

C Dodge, R Schneider, C Sander. The HSSP database of protein stiaicture-sequence alignments and family profiles. Nucleic Acids Res 26 313-315, 1998. 

For each fold one searches for the best alignment of the target sequence that would be compatible with the fold the core should comprise hydrophobic residues and polar residues should be on the outside, predicted helical and strand regions should be aligned to corresponding secondary structure elements in the fold, and so on. In order to match a sequence alignment to a fold, Eisenberg developed a rapid method called the 3D profile method. The environment of each residue position in the known 3D structure is characterized on the basis of three properties (1) the area of the side chain that is buried by other protein atoms, (2) the fraction of side chain area that is covered by polar atoms, and (3) the secondary stmcture, which is classified in three states helix, sheet, and coil. The residue positions are rather arbitrarily divided into six classes by properties 1 and 2, which in combination with property 3 yields 18 environmental classes. This classification of environments enables a protein structure to be coded by a sequence in an 18-letter alphabet, in which each letter represents the environmental class of a residue position. 

B. Schematic representation of the channel aligned with the free energy profile above and indicating the direction of the field. Reproduced with permission from Ref. 45)... 

A Hidden Markov Model (HMM) is a general probabilistic model for sequences of symbols. In a Markov chain, the probability of each symbol depends only on the preceding one. Hidden Markov models are widely used in bioinformatics, most notably to replace sequence profile in the calculation of sequence alignments. 

The aim of the fust dimension breadth is to reveal sequence-function relationships by comparing protein sequences by sequence similarity. Simple bioinformatic algorithms can be used to compare a pair of related proteins or for sequence similarity searches e.g., BLAST (Basic Local Alignment Search Tool). Improved algorithms allow multiple alignments of larger number of proteins and extraction of consensus sequence pattern and sequence profiles or structural templates, which can be related to some functions, see e.g., under http //www. expasy.ch/tools/ similarity. 

A sequence profile represents certain features in a set of aligned sequences. In particular, it gives... 

Stelzer et al. [109] have studied the case of a nematic phase in the vicinity of a smooth solid wall. A distance-dependent potential was applied to favour alignment along the surface normal near the interface that is, a homeotropic anchoring force was applied. The liquid crystal was modelled with the GB(3.0, 5.0, 2, 1) potential and the simulations were run at temperatures and densities corresponding to the nematic phase. Away from the walls the molecules behave just as in the bulk. However, as the wall is approached, oscillations appear in the density profile indicating that a layered structure is induced by the interface, as we can see from the snapshot in Fig. 19. These layers are... 

The angular momentum conservation equation couples the viscous and the elastic effects. The angular profiles of the director and the effective viscosity data are computed for one set of material parameters based on published data in literature. The velocity profiles are also attained from the same dataset. The results show that the alignment of molecules has a strong influence on the lubrication properties. 

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