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Consistent Sets of Secondary Structures in Proteins
Algorithmica, 2007zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Piotr Berman, Jieun K. Jeong
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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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Comparison of Super-secondary Structures in Proteins
Journal of Molecular Biology, 1973Abstract A method of comparing the conformations of different, but structurally related proteins is described. Local variations, such as the systematic translation of a helix, or the position of deletions and insertions can be detected, and the correspondence of only marginally similar structures can be measured.
S T, Rao, M G, Rossmann
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Modeling secondary structures and secondary structure linkages of protein sequences
2010 IEEE International Conference on Systems, Man and Cybernetics, 2010In this paper we model protein secondary structures such as a-helices and b sheets and linkages thereof using passive electrical circuit components and obtain the frequency responses of these circuits. An analysis of the frequency responses of these model circuits shows that putative connections can be made between circuit behavior and known ...
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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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The role of secondary structure in protein structure selection
The European Physical Journal E, 2010The presence of highly regular secondary structure motifs in protein structure is a fascinating area of study. The secondary structures play important roles in protein structure and protein folding. We investigate the folding properties of protein by introducing the effect of secondary structure elements. We observed the emergence of several structures
Yong-Yun, Ji, You-Quan, Li
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Uncertainty Visualization for Secondary Structures of Proteins
2018 IEEE Pacific Visualization Symposium (PacificVis), 2018We present a technique that conveys the uncertainty in the secondary structure of proteins—an abstraction model based on atomic coordinates. While protein data inherently contains uncertainty due to the acquisition method or the simulation algorithm, we argue that it is also worth investigating uncertainty induced by analysis algorithms that precede ...
Christoph Schulz 0001 +5 more
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On the pathway of the formation of secondary structures in proteins
Proteins: Structure, Function, and Bioinformatics, 2023AbstractProtein structures are typically made up of well‐defined modules, called secondary structures. A hierarchical model of protein folding may start with the formation of five‐membered non‐covalently‐linked ring motifs involving O⋅⋅⋅C=O and N−H···N interactions connecting two consecutive peptide groups.
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Evaluation of secondary structure predictions in proteins
Biochimica et Biophysica Acta (BBA) - Protein Structure, 1977Data of 33 proteins are used to compare four methods which predict secondary structure from the amino acid sequence. The prediction of alpha-helices according to the histogram method of Argos et al. (Argos, P., Schwarz, J. and Schwarz, J. (1976) Biochim. Biophys.
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The protein secondary structure flexibility
2008Modeling protein flexibility is a long standing challenge in computational biology with a special impact to protein docking. Relating problems are protein structures alignment and identification of flexible and rigid protein regions, as well as a general definition of a region degree of flexibility.
Šikić, Krešimir +2 more
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