Protein sequence-structure

G Vriend, C Sander, PFW Stouten. A novel search method for protein sequence-structure relations using property profiles. Protein Eng 7 23-29, 1994. 

To gain the most predictive utility as well as conceptual understanding from the sequence and structure data available, careful statistical analysis will be required. The statistical methods needed must be robust to the variation in amounts and quality of data in different protein families and for structural features. They must be updatable as new data become available. And they should help us generate as much understanding of the determinants of protein sequence, structure, dynamics, and functional relationships as possible. 

RH Lathi op, IR Rogers Ir, TE Smith, IV White. A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment. Bull Math Biol 60 1039-1071, 1998. 

Swiss-Prot ia a curated databank of information on protein sequence, structure and function. It can be found under http //www.ebi.ac.uk/swissprot/. 

Catherinot, V. and Labesse, G. (2004) VITO tool for refinement of protein sequence-structure alignments. Bioinformatics, 20 3694-3696. 

Structural proteomics aims the determination of three-dimensional protein structures in order to better understand the relationship between protein sequence, structure, and function. NMR and x-ray crystallography have been significant methods and indispensable tools to determine the structure of macromolecules, especially proteins. Many biotechnology companies have been using these two techniques for enlightening protein structure (Table 5.5). 

Another recent trend is to show the importance of hydrophobic profiles rather than molecular hydrophobicity. Giuliani et al. (2002) suggested nonlinear signal analysis methods in the elucidation of protein sequence-structure relationships. The major algorithm used for analyzing hydrophobicity sequences or profiles was recurrence quantification analysis (RQA), in which a recurrence plot depicted a single trajectory as a two-dimensional representation of experimental time-series data. Examples of the global properties used in this... 

Giuliani, A., Benigni, R., Zbilut, J.P., Webber, C.L. Jr, Sirabella, P and Colosimo, A. 2002. Nonlinear signal analysis methods in the elucidation of protein sequence-structure relationships. Chem. Rev. 102 1471-1492. 

Eisenberg, D., Bowie, J.U., Luthy, R., Choe, S. Three-dimensional profiles for analysing protein sequence-structure relationships. Faraday Discuss. Chem. Soc. 1992, 25-34. 

Molecular Database Nucleotide Sequences Protein Sequences Structures... 

It is much easier and quicker to produce sequence information than to determine 3D structures of proteins in atomic detail. As a consequence, there is a protein sequence/structure deficit. In order to benefit from the wealth of sequence information, we must establish, maintain, and disseminate sequence databases provide user-friendly software to access the information, and design analytical tools to visualize and interpret the structural/functional clues associated with these data. 

Sequences of the representative proteins are displayed in JOY protein sequence/ structure representation (http //www-cryst.bioc.cam.ac.uk/ joy/). The representations are uppercase for solvent inaccessible, lowercase for solvent accessible, red for a helix, blue for strand, maroon for 310 helix, bold for hydrogen bond to main chain amide, underline for hydrogen bond to main chain carbonyl, cedilla for disulfide bond, and italic for positive angle. The query sequence is displayed in all capital letters. The consensus secondary structure (a for a helix, b for strand, and 3 for 310 helix) as defined, if greater than 70% of the residues in a given position in that particular conformation, is given underneath. 

Lindqvist, Y., and Schneider, G. (1997). Circular permutations of natural protein sequences structural evidence. Curr. Opin. Struct. Biol, 7, 422—427. 

Iakoucheva LM, Dunker AK (2003) Order, disorder, and flexibility Prediction from protein sequence. Structure (London) 11 1316-1317... 

Hanisch, D., R. Zimmer and T. Eengauer, ProML - the Protein Markup hanguage for specification of protein sequences, structures and families, Proceedings GCB2001, to appear. 

Wilson, C. A., J. Kreychman, and M. Gerstein. 2000. Assessing annotation transfer for genomics Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J Mol Biol 297 233 49. 

Lin, K., May, A.C.W., Taylor, W.R. Threading using neural network (TUNE) The measure of protein sequence-structure compatibility. Bioinformatics 2002,18,1350-7. 

There is a considerable impetus to predict accurately protein structures from sequence information because of the protein sequence/structure deficit as a consequence of the genome and full-length cDNA sequencing projects. The molecular mechanical (MM) approach to modeling of protein structures has been discussed in section 9.2, and the protein secondary structure prediction from sequence by statistical methods has been treated in section 9.5. The prediction of protein structure using bioinformatic resources will be described in this subsection. The approaches to protein structure predictions from amino acid sequences (Tsigelny, 2002 Webster, 2000) include ... 

The best operative conditions to separate the 20 natural amino acids by using a wide variety of commercially available stationary phases used both in normal and in reversed-phase chromatography and by two-dimensional (2D) chromatography technique are described. Resolution of amino acids derivatives, which play a fundamental role in the peptide and protein sequence structures, is also reported. 

Protein structure-function protein sequence-structure networks (kinetic, regulatory, signaling) bioinformatics dynamics in solvent environment... 

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