Structural Alphabet (SA)
Mining protein loops using a structural alphabet and statistical exceptionality.
... using structural motifs without restriction on loop ...the structural alphabet ...called structural letter. The difficult task of the structural grouping of huge data sets is thus ...
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Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight
... on structural variability ...Multiple structural alignment tools, such as MUSTANG [ 13 ] and MulPBA programs [ 14 ], are proposed to compare globally 3D ...local structural variability. CoDNaS ...
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Use of a structural alphabet for analysis of short loops connecting repetitive structures.
... Each PB is a fragment five residues long that corresponds to a local fold and is defined by eight dihedral angles. PBs m and d correspond roughly to the core of α-helices and β-strands, respectively. In the example in ...
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Protein structure analysis, prediction and flexibility in the light of a structural alphabet
... Structural alphabet : prediction of flexibility 71 PredyFlexy predicts from the sequencethe protein flexibility, this last being defined from data coming from X-ray structures and molecular dynamics ...
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Structural Alphabet: From a Local Point of View to a Global Description of Protein 3D Structures
... the structural alphabet is a tool for analyzing local protein structures, so allowing one to work with a chain of characters rather than with carbon α ...a structural alphabet facilitates the ...
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Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet
... NMR, NMR alone, SAXS alone and molecular dynamics [ 38 – 48 ] and have been analyzed in [ 36 ]. 2.2. N eq Entropy Index Protein blocks (PBs) are the most widely-used structural alphabet composed of 16 local ...
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Exploring the use of a structural alphabet for a structural prediction of protein loops
... How ecient can one expect the loop conformation prediction ? Our scores are dicult to compare with the results of other approaches, usually in terms of RMS deviations between the predicted conformation - i.e. one ...
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iPBA: a tool for protein structure comparison using sequence alignment strategies.: Structural Alphabet Alignment
... tural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide con- formations that can fairly approximate a complete protein ...PB-based structural alignments ...
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Improvement of protein structure comparison using a structural alphabet.
... A structural alphabet consisting of 16 pentapeptide motifs called Protein Blocks (PBs) was developed in our laboratory {de Brevern, 2005 #62; de Brevern, 2000 ...character alphabet ranging from a to ...
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Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship.
... several structural data banks. Depending on the author, the number of structural frag- ments used may range from four to ...“structural alphabet” (Unger et ...precise structural ...
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Global analysis of VHHs framework regions with a structural alphabet: VHH FRs structures
... systematic structural analyses had been performed on VHH structures despite a significant number of ...the structural diversity of FRs of VHHs. Using a structural alphabet that allows ...
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New assessment of a structural alphabet.
... Secondary structures: The columns 9 to 14 sum up the secondary structure assignments done by PSEA [16] and STRIDE [17]. In our previous work [6], the assignment was done with a consensus method [18] based on other ...
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Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.: species‟ sequence - structure relationship
... PB structural alphabet have also given successful results (de Brevern et ...our structural alphabet have been compared with those of 8 other structural ...PB alphabet is highly ...
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Structural deformation upon protein-protein interaction: A structural alphabet approach
... same structural modifications be observed in unrelated proteins ? Could we use the qualitative descrip- tion of structural changes to make a classification of bind- ing movements ? An example of such ...
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Species specific amino acid sequence - Protein local structure relationships: An analysis in the light of a structural alphabet
... of structural models (de Brevern, 2010; Kelley and Sternberg, 2009), are mainly based on machine learning algorithms (Brylinski and Skolnick, 2008; Rangwala et ...
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Développement d'un alphabet structural intégrant la flexibilité des structures protéiques
... and structural fluctuations occurring within fully assembled 236 complexes ...new structural alphabet, SAFlex, improved from HMM-SA, with similar fragment descriptors, 241 number of letters (27), ...
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On the supports of recognizable series over a field and a single letter alphabet
... 2. Preliminaries Basic notions on (recognizable) languages and finite automata are supposed to be known. The reader can refer to [8] for details. Remind in particular that recognizable languages over a single letter ...
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A reduced amino acid alphabet for understanding and designing protein adaptation to mutation.
... Positions 23 and 184 in 2S3 are Q23L and M184L are with PB m, a Protein Block known to be extremely stable and associated to helical structures. Q23L resulted in the highest contribution to oxidative stability in the ...
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Continuity of the Hausdorff Measure of Continued Fractions and Countable Alphabet Iterated Function Systems
... 4. Short Preliminaries on Conformal Iterated Function Systems Let (X, ρ) be a compact metric space. Let E be a countable set, either finite or infinite, called in the sequel an alphabet. Fix a number s ∈ (0, 1). ...
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Inversion of polynomial systems and separation of nonlinear mixtures of finite-alphabet sources
... [36], [22], [5], [4], [6]. On the other hand, the case of sources in a discrete or finite alphabet has been considered for long [37], [47], [23], [25] and the strength of the discrete sources assumption has been ...
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