Sequence Alignment and Modeling

Hughey, R., Krogh, A., Barrett, C., and Grate, L. (1996). SAM Sequence alignment and modelling software. University of California, Baskin Center for Computer Engineering and Information Sciences, http //www.cse.ucsc.edu/research/compbio/papers/sam doc/sam doc.html)... 

Sequence Alignment and Modeling System With Hidden Markov Models... 

Other sources of sequences can be simply drawn from published data sets, but it is important to perform further TF binding modelling using appropriate software packages such as the Sequence Alignment and Modelling System (SAM), http //www.cse.ucsc.edu/research/compbio/sam.html (for example used for the transcription factor AP-2 [19]. 

The superfamily of plant, fungal, and bacterial heme peroxidases (also called non animal peroxidase superfamily, see Chap. 2) categorizes its components into three classes based on sequence alignment and biological origin, such as initially proposed by K.G. Welinder using the only crystal structure available at that moment (yeast CCP) as a model [3, 4]. Class III is the largest one, with over 3,000 plant peroxidase entries in PeroxiBase, followed by Classes I and II, with over 900 entries... 

A search for Oxford Molecular Ltd., which produces a variety of software for sequence alignment, molecular modeling of antibodies, QSAR, semiempirical molecular orbital calculations, and so on, yielded five hits in CJACS through 1993. A search for CompuDrug produced a total of two hits, one in 1990 and one in 1992. 

Liu, J., Neuwald, A., and Lawrence, C. (1995) Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. J. Amer. Stat. Assoc. 90, 1156-1170. 

Sequence alignment and homology modeling. Sequence alignment and homology modeling were done using Ebi (www.ebi.ac.uk) and WISS-PROT (http //swissmodel.expasy.org/) servers. 

In summary, there is no simple correlation between the occurrence of peripheral ion pairs and thermal stabilization. Even after carefiil selection of specific loci for site-directed mutagenesis on the basis of multiple sequence alignments and homology modeling, the results are not clearly predictable. If we recall that the overall stability of proteins is a minute difference between large contributions of attractive and repulsive forces and the corresponding entropy contributions, this result is not surprising. 

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