Database search methods

Secondary sources of patent information, Advances in patent documentation. Types of patent information searches. On-line database searching methods. Cross-file and multifile techniques. 

To overcome the limitations of the database search methods, conformational search methods were developed [95,96,109]. There are many such methods, exploiting different protein representations, objective function tenns, and optimization or enumeration algorithms. The search algorithms include the minimum perturbation method [97], molecular dynamics simulations [92,110,111], genetic algorithms [112], Monte Carlo and simulated annealing [113,114], multiple copy simultaneous search [115-117], self-consistent field optimization [118], and an enumeration based on the graph theory [119]. 

GD Schuler. Sequence alignment and database searching. Methods Biochem Anal 39 145-171, 1998. 

Kurogi Y, Miyata K, Okamura T, Hashimoto K, Tsutsumi K, Nasu M, Moriyasu M. Discovery of novel mesangial cell proliferation inhibitors using a three-dimensional database searching method. J Med Chem 2001 44 2304-7. 

Correlations in the co-occurrence of domains can assist in the identification of distant members of a protein family that are not detected with significance using standard database searching methods. In all known examples of proteins with Cl and CNH domains, for example, there is an intervening PH domain (Schultz et al., 1998). The only exception to... 

An important aspect of our AI application is the attention paid to including well-established Fortran programs and database search methods into the decision structure of an expert system network. Only certain AI software tools (such as TIMM) effectively handle this critical aspect for the analytical instrumentation field at this time (57-60)> The ability to combine symbolic and numeric processing appears to be a major factor in development of multilevel expert systems for practical instrumentation use. Therefore, the expert systems in the EXMAT linked network access factor values and the decisions from EXMATH, an expert system with chemometric/Fortran routines which are appropriate to the nature of the instrumental data and the information needed by the analyst. Pattern recognition and correlation methods are basic capabilities in this field. 

Kaminski, J.J., Rane, D.F., Snow, M.E., Weber, L, and Rothofsky, M.L Identification of novel farnesyl protein transferase inhibitors using three-dimensional database searching methods./. Med. Chem. 1997, 40, 4103-4112. 

In our laboratory, we have developed a novel MALDI-MS based assay in combination with separation techniques to rapidly identify and confirm the presence of viral proteins (immature or mature) and impurities in the rAd vector [138], The approach combines powerful multidimensional analytical techniques to fully characterize viral proteins, including RP-HPLC, SDS-PAGE, MALDI-MS, MS/MS, and database searching methods (Figure 19-24). This assay involves dissociation/separation of intact viruses by RP-HPLC, separation of the SDS-dissociated viruses by SDS-PAGE, and enzymatic digestion of the dissociated viral proteins from the RP-HPLC fractions and the gel bands, followed by MALDI-MS, MALDLpost source decay (PSD) studies, and database search. 

To bypass the problems of conventional database search methods, a number of strategies for unrestricted PTM identification have been developed, such as multistep database search, sequence tag by de novo sequencing, and spectral matching approaches (reviewed in Table 2). 

Homologue(s) of known structure (template(s)) determined by database search methods (BLAST, PSI-BLAST, intermediate-sequence-search methods, HMM s, fold recognition methods)... 

Since paralogs are typically more distantly related than orthologs, their detection frequently requires sensitive protein comparison methods such as profiles or HMMs. Even the detection of orthologs can, under some circumstances, require sophisticated database searching methods, e.g. if the corresponding organisms belong to very distant phyla. 

Kaminski JJ, Rane DF, Snow ME, Weber L, Rothofsky ML, Anderson SD, Lin SL. Identification of novel famesyl protein transferase inhibitors using three-dimensional database searching methods. J Med Chem 1997 40 4103 4112. 

D. Builders, Growers, and Linkers In a broader sense, the 3D database searching methods... 

Jagtap P, Goslinga J, Kooren JA, et al. A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies. Proteomics. 2013 13 1352-7. doi 10.1002/pmic.201200352. 

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