Protein local structure prediction
In silico prediction of protein flexibility with local structure approach
... the protein sequence alone through a local 3D structure ...of protein structures with a different view on their flexibility combining both experimental and simulation data (ii) integrates an ...
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A new prediction strategy for long local protein structures using an original description.
... for protein local structure prediction using LSPs, ii) the proposal of an index for directly assessing the relevance of the prediction at each sequence site and iii) the evaluation of ...
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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
... NR prediction rate ...the prediction, better prediction rates were obtained for the test sets from the same species (see supplementary material ...The prediction rates were highly sensitive to ...
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Development of chemogenomic approaches for prediction of protein - ligand interactions
... molecular structure and the biological ...to local minima ...of local minima, to prevent overfitting, and to offer a better control of the generalization error ...
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Supervised learning to tune simulated annealing for in silico protein structure prediction
... of local minima ...candidate structure at its intermediate steps, we propose to adapt this distribution to the protein structure optimization problem by using supervised learning on a sample ...
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Supervised learning to tune simulated annealing for in silico protein structure prediction
... Better efficiency may be expected if learning could take into account global information (in this work, local information is used). • Future work includes – optimization: fine tuning of parameters, other ...
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Species specific amino acid sequence - Protein local structure relationships: An analysis in the light of a structural alphabet
... functions. Prediction of different features of protein structure like secondary structures (Jones, 1999; Madera et ...2002), protein disorder (Madera et ...2010), protein flexibility ...
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Local backbone structure prediction of proteins.
... called Protein Blocks ...the local 3D structure of proteins from the sole knowledge of their ...a protein sequence and performs a prediction in terms of ...The prediction results ...
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The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools.
... experimental structure and comparing it with its de novo design ( ...and local-global alignment (LGA = ...secondary structure level? Largely, the answer is no ( Support- ing ...final ...
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Unfolding RNA 3D structures for secondary structure prediction benchmarking
... The third group of approaches rely on γ-centroid estimators, integer programming and other heuristics. CentroidFold (version 0.0.15) predicts secondary structures us- ing γ-centroid estimators [88]. This corresponds to ...
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CSA: Comprehensive comparison of pairwise protein structure alignments
... CSA: Comprehensive comparison of pairwise protein structure alignments 11 Figure 2: A radar chart for comparison of alignment scores for six different alignments of 1otrA and 2di0A. The closer a point is to ...
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Protein structure determination using NMR backbone chemical shifts
... rapid protein 3D structure determination using simultaneously these three methods and to determine the most probable structure using our optimization evaluation ...
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Rapid protein structure determination using experimental NMR data
... Rapid protein structure determination using experimental NMR data.. Marius Wanko2[r] ...
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Influence of assignment on the prediction of transmembrane helices in protein structures.
... HLA-B27 protein, a Class I Histocompatibility Antigen (HLA-B*2705, PDB code 1HSA (Madden et ...the protein structures in terms of secondary structure assignment with different secondary ...
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Computational prediction of coiled-coil interaction structure specificity
... This thesis describes our recent work in updating statistical coiled- coil prediction methods using new sequences, introducing more stringent tests of method performance a[r] ...
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Multi-dimensional probing for RNA secondary structure(s) prediction
... the prediction model, has shown to allow for highly accurate secondary structures compared to the prediction modeling guided by a single probing ...measure local nucleotide flexibility, of NMIA-SHAPE ...
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Dynamics of protein structures and its impact on local structural behaviors
... helix enjoy status of being special cases of secondary structure elements which occur at different Φ, Ψ values than the regular helices and sheets [18,19]. β-sheets are formed by arrangement of β- strands in ...
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Structure-function insights into elusive Mycobacterium tuberculosis protein Rv1916
... recombinant protein corresponding to expected size of ~47 kDa on SDS- polyacrylamide ...recombinant protein is localized in the insoluble fraction of the lysate ...expressed protein was purified by ...
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Local Skeleton Discovery for Incremental Bayesian Network Structure Learning
... Thus how to achieve optimum results under various resource constraints becomes a challenging task. Bayesian network (BN) is a graphical representation for joint probability distribution among a set of random variables. ...
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Improvement of protein structure comparison using a structural alphabet.
... of local alignments with a high alignment score can help in finding conserved stretches in the ...non-overlapping local alignments, the SIM algorithm developed by Huang and Miller {Huang, 1991 #94} was used ...
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