Structure superposition

Diederichs, K. Structural superposition of proteins with unknown alignment and detection of topological similarity using a six-dimensional search algorithm. Proteins Struc., Func., Genet. 1995, 23, 187-195. 

Finding a mapping between the atoms of the equivalent proteins is a preliminary step before the structural superposition. There are many ways of finding a mapping between a pair of macromolecu-lar targets. I will describe two of them in the following section. 

Fig. 5. Structural superposition of binding sites using Med-Sumo . The Surface Chemical Features (SCF) are used to superimpose the protein binding sites (toppanel).The SCF are represented in color code bar (bottom panel) and the SUMO score measure the quality of the 3D structural superimposition that is calculated using a bit-wise matching algorithm of the color code-bar fingerprint (bottom panel).

Significant efforts have been made to assemble teratogenic data basses with peer-reviewed evaluations (ref. 1). New avenues for the SAR studies have been opened, such as quantitative methods for structural superposition of molecules and for superposition of their reactivity characteristics (ref. 2). Emphasis has been placed on the electrostatic properties of the molecules, such as the molecular electrostatic potential, the electric fields, and the polarizability terms calculated from perturbation expansions (ref. 2). Computer-assisted multivariate SAR which deals with many variables simultaneously has been advanced (ref. 3). 

Structure superposition and alignment Computing activities and properties of molecules often involves comparisons across a homologous series. Such techniques require superposition or alignment of structures. 

Structural superposition of ILlOFMs domains were performed by using Dali (Holm and Sander, 1995, 1999) and refined by the method of Rao and Rossman as implemented in SUPPOS (Fig. 5). Using IL-10 as a reference, the viral IL-lOs are most similar to IL-10 followed by IL-19, IL-22, and IFN-7, respectively (Table IV). The comparisons reveal a common helical core centered on the bend in helix F (Fig. 5). Residues with... 

Structure comparison methods are a way to compare three-dimensional structures. They are important for at least two reasons. First, they allow for inferring a similarity or distance measure to be used for the construction of structural classifications of proteins. Second, they can be used to assess the success of prediction procedures by measuring the deviation from a given standard-of-truth, usually given via the experimentally determined native protein structure. Formally, the problem of structure superposition is given as two sets of points in 3D space each connected as a linear chain. The objective is to provide a maximum number of point pairs, one from each of the two sets such that an optimal translation and rotation of one of the point sets (structural superposition) minimizes the rms (root mean square deviation) between the matched points. Obviously, there are two contrary criteria to be optimized the rms to be minimized and the number of matched residues to be maximized. Clearly, a smaller number of residue pairs can be superposed with a smaller rms and, clearly, a larger number of equivalent residues with a certain rms is more indicative of significant overall structural similarity. 

Overview of the 3D-PSSM approach for protein structure prediction For any protein (superfamily) PSI-BLAST searches and profiles are computed and using the structural superposition of the (structurally related) family members. On the basis of... 

Swiss-PDBViewer Structure, superposition, alignment and modelling visualization http //www.expasy.ch/spdbv/ SIB, CH, N. Guexetal. [308]... 

Maiti, R, G. H. Van Domselaar, H. Zhang, and D. S. Wishart. 2004. SuperPose A simple server for sophisticated structural superposition. Nucleic Acids Res 32 W590-4. 

Figure 23 Structural superposition of lumazine protein (green, PDB entry code 3DDY ) and riboflavin synthase from Schizosaccharomycespombe (yellow, PDB entry code 1KZC ). The C-terminal segment of riboflavin synthase is marked by red color.

For each set of loops, all examples were extracted from the Brookhaven Data Bank [7] and characterized according to loop length, 0, y/ conformation, sequence and structural superposition. The distribution of loop lengths (Figure 15.4) shows that nearly 70% have five or less residues. The loops that form structural families are indicated by shading in Figure 15.4 and summarized in Table 15.2. As expected, the families occur in the very short loops, where the number of possible conformations is small. These families are described in detail by Thornton and coworkers [22], and here we present just one family from each supersecondary group, as an example of the sorts of pattern observed. 

Structural alignment of the basis structures There are many algorithms for performing structural superposition (e.g. Sali andBlundell ). This structure-based alignment is vital to elucidate conserved structural and sequence features. 

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