Database Method

K Fidelis, PS Stern, D Bacon, I Moult. Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng 7 953-960, 1994. 

Standard methods Template structure identification Databases Method development (molecular structure) Qualitative and quantitative analysis... 

Three popnlar early methods are dne to Chon and Fasman, Ganuer et al., and Lim." ° The Chon-Fasman method is based on statistical propensities of residues to form an a-helix or a P-strand, combined with a series of rules. Many methods, like Chon-Fasman, are based on statistical analyses of structural databases. The GOR method adopts an information theory approach. Although the theory is a little daunting, this is transparent to the user and the method has a firm statistical foundation that permitted extension to more subtle analyses of a larger structural database." Methods may also be based on the physico-chemical principles underlying protein structure. For example, a-helices often have a distinct pattern of hydrophobic residues, leading to a hydrophobic face that can facilitate the packing of the helix in the protein. A series of such rules forms the basis of the Lim method. ... 

In recent years, as the size of the PDB has increased, database methods have continued to attract attention. With a larger database, recurring structural motifs have been classified for loop structures [111, 114, 116, 129, 134], including their sequence dependence. Database methods have been applied only for loops of up to 8 residues. Fidelis et al. [126] found that for loops of length greater than 7 there is not likely to be a segment in the PDB that corresponds to the correct loop conformations for the 58 protein they looked at. Some authors report that when the database contains a loop of similar structure to the target to be modeled, their methods perform well, with RMSD values around 1A or better. Otherwise they tend to fail [124, 127, 130]. 

Apart from complete modeling packages (discussed below), only a small number of programs are freely and publicly available from the many methods that have been published (see Table 5.6). Among database methods, this includes only Swiss-PDBViewer [151], and BRAGI which implements the method of Fechteler et al. [128]. Several loop databases are available. Among... 

Peitsch, Guex [151, 196] SwissModel GROMOS Alignment determines core backbone, while loops are built with database method. Side chains are built using the template side chain where possible, and GROMOS minimization otherwise. 

Database method remains limited improvement over CASP1... 

Wootton, J. C. and Federhen, S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266, 554-571 http //www.ncbi.nlm.nih.gov/books/bv.fcgi rid=handbook.chapter.chl6. 

Orengo, C. A., F. M. Pearl, and J. M. Thornton. 2003. The CATH domain structure database. Methods Biochem Anal 44 249-71. 

We would predict, then, that the next decade will see a significant increase in the development of knowledge acquisition methodologies applied to crystallographic databases. Methods for the representation, storage and application of this knowledge will soon become a necessity and then a reality. 

J., Bond, P.J., Whitmore, A.V., Zimmer, S., Young, M.P., Jenkins, J.L., Glick, M., Glen, R.C., and Bender, A. (2011) From in silico target prediction to multi-target drug design current databases, methods and applications. /. Proteomics, 74, 2554-2574. 

Keimy PW, Sadowski J. Structure modification in chemical databases. Methods Princ Med Chem 2005 23 271-285. 

An instantiation of the Minimal (respectively NonMinimal) predicate-variable tests whether the induction parameter is of a minimal (respectively non-minimal) form. These forms must be mutually exclusive over the domain of the induction parameter. Step 2 yields LAiir) by first selecting an induction parameter, and then instantiating the Minimal and NonMinimal predicate-variables by means of a so-called Database Method, which here relies on a database of type-specific form-identifying formulas. 

An instantiation of the Decompose predicate-variable deterministically decomposes, in the non-minimal case, the induction parameter, say X, into a vector HX of heads and a vector TX of tails, the tails TXj being smaller than X according to some well-founded relation. These tails are meant for the recursive computation of the tails TYj of the other parameter, say Y. Step 3 yields LA ir) by instantiating the Decompose predicate-variable by means of the Database Method, which here relies on a database of type-specific decomposition formulas. 

Third, the methods used by Steps 2 and 3 could be abstracted into a Database Method. This would work as follows given an example set , some computations C, and a database DB, select an entry from DB using the key generated by executing C on E. 

How to detect that recursion is useless in some non-minimal sub-cases Step 4 (Syntactic introduction of the recursive atoms) creates a non-recursive case if at least one example Ej leads to a non-admissible procComp(,,yp atom. Howto invent or re-use appropriate predicates How to implement invented predicates The predicate invention problem is tackled at four points during the synthesis. At Steps 2 and 3, the Database Method re-uses predefined predicates this amounts to using domain knowledge. At Step 6, the Synthesis Method (see Section 14.2.4 below) invents new composition operators. As of now, there is no method yet of re-using common composition operators. At Step 7, the PaP Method synthesizes discriminants that are in terms of predicates other than rfn. How to discover which parameters are auxiliary parameters Due to our restriction to version 3 of the divide-and-conquer schema, auxiliary parameters are not taken into account. See Section 14.2.2 below on how to achieve this. 

Methods in this category include the early algorithms of Dean, Lewis, Leach et al., CAVEAT,HOOK, SPLICE and related programs, NEWLEAD,"> PRO LIGAND, 06- 7 ELANA,i and the artificial intelligence approach of Cohen and Shatzmiller.i In addition, there are various 3D database methods ... 

Anick DJ (2003) Application of database methods to the prediction of B3LYP-optimized polyhedral water cluster geometries and electronic energies. J Chem Phys 119 12442-12456... 

Approaches that try to explore all degrees of freedom of the ligand systematically comprise conformational search methods, fragmentation methods or database methods. By applying... 

A computationally efficient way to search for possible orientations forms the database method. For this protocol a conformational library of the ligand is prepared which is docked rigidly into the binding site. 

Griffiths-Jones S (2006) miRBase the microRNA sequence database. Methods Mol Biol 342 129-138... 

Perdeuterated A,a-dimethylbenzylamine (105-DMBA) can be used in a database method to assign the absolute configuration of 1,3,5-triols and 2-methyl-l,3-diols. The DMBA functions as a chiral solvating agent, and the H and C NMR spectrum of each possible diastereomer is recorded and used to prepare a set of patterns for the different isomers. One possibility is to use the pattern of values to assign the absolute configuration. " ... 

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