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Protein secondary structure prediction
Current Opinion in Structural Biology, 1995The past year has seen a consolidation of protein secondary structure prediction methods. The advantages of prediction from an aligned family of proteins have been highlighted by several accurate predictions made 'blind', before any X-ray or NMR structure was known for the family.
S R, Krystek, W J, Metzler, J, Novotny
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Secondary Structure and Protein Deamidation
Journal of Pharmaceutical Sciences, 1999The deamidation reactions of asparagine residues in alpha-helical and beta-turn secondary structural environments of peptides and proteins are reviewed. Both kinds of secondary structure tend to stabilize asparagine residues against deamidation, although the effects are not large.
M, Xie, R L, Schowen
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Protein Secondary Structure Prediction
2009While the prediction of a native protein structure from sequence continues to remain a challenging problem, over the past decades computational methods have become quite successful in exploiting the mechanisms behind secondary structure formation. The great effort expended in this area has resulted in the development of a vast number of secondary ...
Pirovano, W.A., Heringa, J.
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Protein Secondary Structure Prediction with SPARROW
Journal of Chemical Information and Modeling, 2012A first step toward predicting the structure of a protein is to determine its secondary structure. The secondary structure information is generally used as starting point to solve protein crystal structures. In the present study, a machine learning approach based on a complete set of two-class scoring functions was used.
Francesco, Bettella +2 more
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Knowledge‐based protein secondary structure assignment
Proteins: Structure, Function, and Bioinformatics, 1995AbstractWe have developed an automatic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone torsional angle information. Parameters of the pattern recognition procedure were optimized using designations provided by the crystallographers ...
D, Frishman, P, Argos
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Chemogenomics with Protein Secondary-Structure Mimetics
2009During molecular recognition of proteins in biological systems, helices, reverse turns, and beta-sheets are dominant motifs. Often there are therapeutic reasons for blocking such recognition sites, and significant progress has been made by medicinal chemists in the design and synthesis of semirigid molecular scaffolds on which to display amino acid ...
Garland R, Marshall +2 more
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2010
There are several methods available that can be used to gain information on secondary structure, apart from X-ray crystallography, which remains the ‘gold standard’.
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There are several methods available that can be used to gain information on secondary structure, apart from X-ray crystallography, which remains the ‘gold standard’.
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A Grid-Enabled Protein Secondary Structure Predictor
IEEE Transactions on Nanobioscience, 2007We present an integrated Grid system for the prediction of protein secondary structures, based on the frequent automatic update of proteins in the training set. The predictor model is based on a feed-forward multilayer perceptron (MLP) neural network which is trained with the back-propagation algorithm; the design reuses existing legacy software and ...
M. MIRTO +4 more
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PSS-SQL: Protein Secondary Structure - Structured Query Language
2010 Annual International Conference of the IEEE Engineering in Medicine and Biology, 2010Secondary structure representation of proteins provides important information regarding protein general construction and shape. This representation is often used in protein similarity searching. Since existing commercial database management systems do not offer integrated exploration methods for biological data e.g.
Dariusz, Mrozek +3 more
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Multiple Alignment Through Protein Secondary-Structure Information
IEEE Transactions on Nanobioscience, 2005It is well known that protein secondary-structure information can help the process of performing multiple alignment, in particular when the amount of similarity among the involved sequences moves toward the "twilight zone" (less than 30% of pairwise similarity).
Armano G, Milanesi L, Orro A
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