Fold prediction

While this is disappointing, the nonuniqueness theorem also shows that if some empirical potential is able to predict correct protein folds then many other empirical potentials will do so, too. Thus, the construction of empirical potentials for fold prediction is much less constrained than one might think initially, and one is justified in using additional qualitative theoretical assumptions in the derivation of an appropriate empirical potential function. 

Godzik A, A Kolinski and JSkolnick 1993, DeNovo and Inverse Folding Predictions of ProteinStm and Dynamics. Journal of Computer-Aided Molecular Design 7 397-438. 

M Huynen, T Doerks, F Eisenhaber, C Orengo, S Sunyaev, Y Yuan, P Bork. Homology-based fold predictions for Mycoplasma genitalmm proteins. J Mol Biol 280 323-326, 1998. 

L Jaroszewski, L Rychlewski, B Zhang, A Godzik. Fold prediction by a hierarchy of sequence, threading, and modeling methods. Protein Sci 6 1431-1440, 1998. 

Figure 4. Alignment of PelZ and PelC amino acid sequences. The vertical lines indicate identical amino acids and the two points indicate homologous amino acids. The bold letters correspond to the residues probably involved in Ca + binding or catalytic function(s). The two aspartate residues probably involved in Ca binding are indicated with an asterisk. The invariant residues, probably involved in PGA cleavage, are indicated with an open circle. The folding in p-sheets is characterised by the underlined amino acids. Double underlining of PelZ residues is deduced from Chou Fasman and Robson Gamier folding predictions.

Djurdjevic, D.P., and Biggs, N.J., Ab initio protein fold prediction using evolutionary algorithms Influence of design and control parameters on performance, /. Comp. Chem., Tl, 1177,2006. 

In another study of protein structure, Cox and Johnston3 analyzed how the choice of GA parameters affects the quality of the GA search. This sort of approach was also adopted by Djurdjevic and Biggs,4 who presented a detailed study of how evolutionary algorithms can be used, in combination with a full atomistic protein ab initio model, for fold prediction and, like Cox and Johnston, considered the influence of the different values of parameters on the success of their protein folding calculations. 

Fig. 3. The protein fold recognition protocol and fold prediction for complete genomes, (a) Construction of the FID library (b) fold prediction for proteins encoded in complete genomes. 

The number of genes annotated in this genome is unusually large given the genome size. Thus we suspect that many of the annotated open reading frames are not real genes, which results in an unexpectedly low rate of fold prediction. 

The fold prediction rate achieved in this analysis is an even greater improvement over the results achieved with pairwise alignment methods (Fischer and Eisenberg, 1997 Gerstein and Levitt, 1997) than reported previously (Wolf et al., 1999). By contrast, several more recent studies that applied PSSM-based methods to protein sets from individual genomes have reported similar prediction rates (Huynen et al., 1998 Paw-... 

Manual Evaluation of Fold Prediction for Three Genomes... 

Fold predictions for proteins from 22 proteomes are available on the World Wide Web at http //ncbi.nlm.nih.gov/CBBresearch/koonin/FOLDS/. The FIDs are available on request (wolf ncbi.nlm.nih.gov). 

Huynen, M., Doerks, T., Eisenhaber, F., Orengo, C., Sunyaev, S., Yuan, Y., and Bork, P. (1998). Homology-based fold predictions for Mycoplasma genitalium proteins. / Mol. Biol. 280, 323-326. 

Taylor, W., Jones, D., and Green, N. (1994). A method for a-helical integral membrane protein fold prediction. Proteins Struct. Fund. Genet. 18, 281-294. 

The identification of the fold is, however, only a minor part of protein characterization. Function is a loosely defined term, but must be viewed within a particular context, e.g., protein function can only take place with an interaction partner or within cellular cascades and networks. Fold predictions and homology searches can only give partial answers to such higher order functions. Thus, independent functional features have to be collected and put into context. Such features include not only molecular properties, but also cellular roles, expression patterns, dysfunctions, pathway context, and subcellular localization. The latter can be predicted by exploiting a variety of methods and localization sites. Kenta Nakai reviews many such sites and their implementation... 

Deckmyn, H. and Preaux, G. 1978. Chain-folding prediction of the bovine, 3-lactoglobu-lin. Arch. Intern. Physiol. Biochim. 86, 938-939. 

Secondary (2°) Local 3D structure (fold) a-helices, P-sheets RNA and protein fold prediction... 

Computation proteome annotation is the process of proteome database mining, which includes structure/fold prediction and functionality assignment. Methodologies of secondary structure prediction and problems of protein folding are discussed. Approaches to identify functional sites are presented. Protein structure databases are surveyed. Secondary structure predictions and pattern/fold recognition of proteins using the Internet resources are described. 

Enter the sequence name, paste the sequence in the query box, select or accept default options, and click the Submit button. The results (thermochemical data in text and plot files, and structure files in various formats including PostScrip) are returned (Figure 14.2). Analogous folding prediction for DNA is available at http //bioinfo.math.rpi.edu/ mfold/dna/form 1. cgi... 

In principle, the protein folding prediction problem can be solved in a very simple way. One could generate all the possible conformations a given protein might assume, compute the free energy for each conformation, and then pick the conformation with the lowest free energy as the correct native structure. This simple scheme has two major caveats. 

Edwards, Y. J. K. and Perkins, S. J., Assessment of protein fold predictions from sequence information the predicted a/ 3 doubly wound fold of the van WUlebrand factor type A domain is similar to its crystal structure, J. Mol Biol, 260, 277, 1996. 

From a historical perspective, there are two main complementary approaches to address RNA folding prediction thermodynamic models and phylogenetic models. 

Although PanK-II enzymes can easily be distinguished from type I PanKs based on the differences in their primary sequences, they also have distinctly different structural folds. The structures of the human PanKfa and PanK3 isoforms and the bacterial PanK-II from S. aureus, as well as structural fold predictions, " " indicate that PanK-II enzymes belong to the acetate and sugar kinase/heat-shock protein 70/actin (ASKHA) superfamily of kinases they are not P-loop kinases like type I PanKs. 

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