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RNAformer: A Simple yet Effective Model for Homology-Aware RNA Secondary Structure Prediction
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Prediction of Packing of Secondary Structure
Advances in Biophysics, 1984An improved method of picking up candidates for predicting the packing arrangement of beta-strands and alpha-helices of the alpha/beta type domains is described here. The method of judging whether the region of the protein would fold into the alpha/beta type or not is also described.
K, Nagano, P K, Ponnuswamy
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On predicting secondary structure transition
International Journal of Bioinformatics Research and Applications, 2007A function of a protein is dependent on its structure; therefore, predicting a protein structure from an amino acid sequence is an active area of research. To improve the accuracy of validation of structures, we are studying the predictability of secondary structure transitions using the following machine learning algorithms: naive Bayes, C4.5 decision
Raja Loganantharaj, Vivek M. Philip
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Improving Protein Secondary-Structure Prediction by Predicting Ends of Secondary-Structure Segments
2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2005Motivated by known preferences for certain amino acids in positions around a-helices, we developed neural network-based predictors of both N and C a-helix ends, which achieved about 88% accuracy. We applied a similar approach for predicting the ends of three types of secondary structure segments.
Uros Midic +2 more
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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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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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In Silico Prediction of RNA Secondary Structure
2017The secondary structure of an RNA molecule represents the base-pairing interactions within the molecule and fundamentally determines its overall structure. In this chapter, we overview the main approaches and existing tools for predicting RNA secondary structures, as well as methods for identifying noncoding RNAs from genomic sequences or RNA ...
Tahi, Fariza +2 more
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Secondary structural predictions for the clostridial neurotoxins
Proteins: Structure, Function, and Bioinformatics, 1994AbstractThe primary structures of a family of ten clostridial. Neurotoxins have recently been deduced yet little information is presently available concerning their secondary or tertiary structures. Because the overall similarity percentage of multiply aligned sequences is high, the secondary structures of these metalloendopeptidases are also expected ...
F J, Lebeda, M A, Olson
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Secondary Structure Prediction for Aligned RNA Sequences
Journal of Molecular Biology, 2002Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation.
Ivo L. Hofacker +2 more
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Redefining the Goals of Protein Secondary Structure Prediction
Journal of Molecular Biology, 1994Secondary structure prediction recently has surpassed the 70% level of average accuracy, evaluated on the single residue states helix, strand and loop (Q3). But the ultimate goal is reliable prediction of tertiary (three-dimensional, 3D) structure, not 100% single residue accuracy for secondary structure.
Chris Sander +2 more
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