protein complexes
Computational prediction of protein protein complexes
... of Protein Structure Prediction (CASP) and Critical Assessment of PRediction of Interactions (CAPRI) community-wide comparative evaluations as well as some preliminary validation studies using known crystal ...
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Factors That Affect the Computational Prediction of Hot Spots in Protein Protein Complexes
... different protein-protein ...16 protein-protein complexes with known crystal ...predictions. Protein-Protein complex interfaces are dynamic and hence conformational ...
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Integrating domain similarity to improve protein complexes identification in TAP-MS data
... detecting protein complexes from the two ...detecting protein complexes, including MCL and ...overlapping protein complexes in PPI networks and experimental results demonstrated ...
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Co-regulation of translation in protein complexes
... average protein production rate of a ...stable protein complexes ...of protein production rates among the subunits of the three yeast ...
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Friedel, Caroline Christina (2009): Analysis of High-Throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life. Dissertation, LMU München: Fakultät für Mathematik, Informatik und Statistik
... individual protein in- teractions are more accurate than previously published scoring methods and the predicted protein complexes achieve the same quality as the best supervised ...confident ...
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Structure and function of mitochondrial membrane protein complexes
... As ubiquitous, semi-autonomous cellular organelles, mitochondria are separated from the cytoplasm by the outer and inner mitochondrial membrane (Fig. 1). The outer membrane is porous and freely traversed by ions and ...
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Models of buffering of dosage imbalances in protein complexes
... induced protein degradation is suppressed when a subunit binds to its partners within a complex ...of protein complexes encoded on the supernumerary chromosome(s) are preferentially buffered at the ...
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Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes
... We have identified the binding sites in protein-protein complexes based on interaction energy as explained in Methods section. We observed that 13.9% of the resi- dues have the interaction energy of ...
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High throughput protein-protein interaction data: clues for the architecture of protein complexes
... of protein-pro- tein interaction (PPI) data on a large ...for Protein Sequences physical interactions, and protein complexes reported in the literature (see Han et ...all complexes in ...
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Identification of protein complexes from multi-relationship protein interaction networks
... multi-relationship protein interaction net- work by integrating PPI networks and GO annotation ...dicting protein complexes, named MINE (based on Multi-relationship protein Interaction ...
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Detecting Protein Complexes by an Improved Affinity Propagation Algorithm in Protein-Protein Interaction Networks
... of protein complexes in protein-protein interaction (PPI) networks is important in understanding cellular ...discover protein complexes with high precision by compared with the ...
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Identifying protein complexes with fuzzy machine learning model
... discovers complexes from the weighted PPI network based on the maximal ...detect protein complexes from PPI networks, where protein-complex cores from the neighbourhood graphs are mined and ...
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Which clustering algorithm is better for predicting protein complexes?
... Six PPI network datasets were subjected to four differ- ent algorithmic strategies. The motivation behind this approach is to benchmark the clustering techniques and measure their prediction accuracy to detect ...
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Discrete Differential Geometry and the Structural Study of Protein Complexes
... In this paper, we propose a novel mathematical toy model which is intended for the structural study of protein complexes. While physics and mathematics have been inspired each other in their long ...
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Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison
... of protein–protein interaction (PPI) data of different species makes it possible to identify common subnetworks (conserved protein complexes) across species via local alignment of their PPI ...
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A Heuristic Ontological Model of Protein Complexes A Case Study Based on the E3 Ubiquitin Ligase Protein Complexes of Arabidopsis thaliana
... a protein complex that forms dependent upon very specific conditions, PRO could be accessed for this particular ...and protein interaction affinities required for a specific E3 ubiquitin ligase to assemble ...
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Spatial chemical conservation of hot spot interactions in protein-protein complexes
... We compared the predictive power of MAPPIS with our previously developed multiple alignment methods. The first method, MultiProt [57] performs multiple structural alignment of the protein backbones represented by ...
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Fluctuations and Entropy in The Energetics and Function of Protein Complexes
... ally symmetric or completely anisotropic depending on the size and shape of the pro- tein [21]. Therefore depending on the tumbling model used, the spectral density func- tion changes and pyRelxn 2A can accordingly be ...
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Structural and Functional Hierarchy in Photosynthetic Energy Conversion—from Molecules to Nanostructures
... molecules through protein complexes to entire organisms [1]. One of the major goals of photosynthesis research, conducted worldwide in academic laboratories and indus- trial institutes, is to find ...
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A graph modification approach for finding core–periphery structures in protein interaction networks
... for protein interaction (PPI) networks assumes that protein complexes in these networks consist of a dense core and a possibly sparse periphery that is adjacent to vertices in the core of the ...
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