Site prediction

Browne, R.G., and Kozlowski, M.R. High affinity 3H-PCP binding sites predict discriminative stimulus properties in rats. In preparation. 

Kalinina OV, Gelfand MS, RusseU RB (2009) Combining specificity determining and conserved residues improves functional site prediction. Bioinformatics. doi 10.1186/1471-... 

It is further worth noting that the observed level of Bac7-resistance is equivalent for the point mutated and null mutants, thus indicating that the point mutation is sufficient to completely abolish its function regarding Bac7 resistance. Significantly, this mutation leads to a Glu to Lys substitution at position 276 at a site predicted to be located between two transmembrane helices, and... 

Predict the splice sites (acceptor and donor sites) of the above nucleotide sequence with WebGene or GenelD and SPL of Sanger Centre. Compare the results of their splice site predictions. 

Catalytic site prediction using manual docking in combination with energy minimizations and/or MD simulations. 

Recently, some more advanced methods have been reported that integrate the disparate features used for the characterization of functional binding sites. It can be expected that the cooperative effect of using all the information available will greatly enhance the reliability of binding site prediction and detection tools. 

From the analyses of many glycosylation sites (GalNAc transferase acceptor sites), a few rules of thumb have been formulated (Wilson et al., 1991) and motif patterns have been proposed (Pisano et al., 1993). Matrix statistics have been compiled for site prediction (Elhammer et al., 1993). However, since there is no clear consensus acceptor sequence pattern and it is strongly influenced by the local conformation, neural network is appropriate for the task. 

Indarte M, Madura JD, Surratt CK (2008) Dopamine transporter comparative molecular modeling and binding site prediction using the LeuT(Aa) leucine transporter as a template. Proteins 70 1033-1046... 

A loose cannon. Sigma protein by itself does not bind to promoter sites. Predict the effect of a mutation enabling a to bind to the -10 region in the absence of other subunits of RNA polymerase. 

Golombek, M.P., et al. Overview of the Mars Pathfinder Mission and Assessment of Landing Site Predictions. Science 278, No. 5344 (December 5,1997) 1743-1748. 

In reaction with the active heme complex, compound 1, it is often assumed that the first stage is homolytic hydrogen abstraction, resulting in radical formation. This is certainly likely to occur with aliphatic hydroxylation. Ideally a calculation of the transition state should be carried out, but this is difficult in practice. Relative radical stabilities have therefore been used as an approximation. In a typical calculation one generates all possible radicals for a substrate, optimizes them, and determines their relative stabilities. They are then docked into the 3D protein structure using constraints between the heme and the sites predicted from the radical calculations. Early descriptions of this approach made use of homology models, but the same techniques can obviously be used with crystal structures. 

---