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[PDF] Top 20 Predicting Protein-Protein Interactions Using BiGGER: Case Studies

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Predicting Protein-Protein Interactions Using BiGGER: Case Studies

Predicting Protein-Protein Interactions Using BiGGER: Case Studies

... between BiGGER and most protein docking software, in that BiGGER was conceived as a tool to help researchers elucidate protein interactions rather than as an automated ...predictor. ... See full document

19

Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction.

Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction.

... SOC1 protein we predicted a loss of 13 of its interaction partners, and for the mutated AGL14 protein a gain of 15 (the difference of two relates to the accuracy of our method for the original interaction ... See full document

13

Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks.

Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks.

... categories using the integrated PPI ...codes using the integrated PPI ...this case, PD DDIs could occur by the close interference between drugs because the drug might directly bind to ... See full document

13

Predicting and validating protein interactions using network structure.

Predicting and validating protein interactions using network structure.

... The Receiver Operating Characteristic (ROC) Curve In order to put our scores to work we choose a threshold; all pairs with scores above that threshold would be classified as interacting, while all pairs below that ... See full document

11

Changes in protein interaction networks between normal and cancer conditions: Total chaos or ordered disorder?

Changes in protein interaction networks between normal and cancer conditions: Total chaos or ordered disorder?

... based studies are needed to bring out more realistic interpretations. Protein interaction network with association of gene regulatory networks would provide more holistic results which are beyond the scope ... See full document

14

Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

... made using the TurboSequest program through the Bioworks Browser ...made using the RefSeq Human Protein Database from NCBI (National Center for Biotechnology Information, Bethesda, MD; release 7) ... See full document

16

In vitro and in vivo studies identify important features of dengue virus pr-E protein interactions.

In vitro and in vivo studies identify important features of dengue virus pr-E protein interactions.

... Here we developed a system to produce DENV pr peptide and reconstitute the pr-E interaction in vitro. At low pH pr bound to both monomeric and dimeric forms of E and blocked their membrane insertion and trimerization. ... See full document

12

Protein-protein interactions in clathrin vesicular assembly: radial distribution of evolutionary constraints in interfaces.

Protein-protein interactions in clathrin vesicular assembly: radial distribution of evolutionary constraints in interfaces.

... heterotetrameric protein complexes [19], are the busiest members of the assembly in terms of the protein partners that they engage and hence, are often termed as hubs of this interaction network ...these ... See full document

11

A feature-based approach to modeling protein-DNA interactions.

A feature-based approach to modeling protein-DNA interactions.

... examined. Using smaller sets which represent under sampling of the TFBS distribution space or sets that contain noise may lead to ...analyses, using a cross validation scheme, on datasets taken from ... See full document

17

Development and Validation of Gold Nanoprobes for Human SNP Detection Towards Commercial Application

Development and Validation of Gold Nanoprobes for Human SNP Detection Towards Commercial Application

... first studies carried out in 90’s that tried to correlate or associate candidate genes to common obesity were heavily relying on their role in the appetite-regulating hormones or their receptors, such as leptin ... See full document

215

DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach.

DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach.

... within protein sequences, GlobPlot [15], was ...a protein sequence based on amino acid composition ...for predicting intrinsically unfolded ...reliably predicting long disordered ...multiple ... See full document

16

Intragenic suppressor of Osiaa23 revealed a conserved tryptophan residue crucial for protein-protein interactions.

Intragenic suppressor of Osiaa23 revealed a conserved tryptophan residue crucial for protein-protein interactions.

... in protein-protein interactions between Aux/IAA and ARF ...families. Studies of other suppressors showed that although baa motif has an important role in dimerization, residues outside of baa ... See full document

9

Arq. NeuroPsiquiatr.  vol.57 número2A

Arq. NeuroPsiquiatr. vol.57 número2A

... The study of cerebrospinal fluid (CSF) is an old tradition in São Paulo. From 1930, Lange and later Reis have undertaken such studies. Later this tradition was kept alive by their collaborators. Lange’s coworkers ... See full document

2

Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function.

Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function.

... Protein-protein interactions (PPIs) are the basis of biological ...the interactions of a protein can help understand its molecular function and its association with different biological ... See full document

10

Preferential Interactions and the Effect of Protein PEGylation.

Preferential Interactions and the Effect of Protein PEGylation.

... PEGylated protein forms a ...scattering studies reported in our previous publication ...the protein unfolding is coupled to dimer dissociation was unsuccessful, failing to reproduce the sharp shape ... See full document

18

Intrinsically disordered caldesmon binds calmodulin via the “buttons on a string” mechanism

Intrinsically disordered caldesmon binds calmodulin via the “buttons on a string” mechanism

... intrachain interactions to fold on their own, but are likely to gain stabilizing energy by interacting with a globular protein partner (Dosztanyi, Meszaros & Simon, 2009; Meszaros, Simon & ... See full document

29

Identification of an FHL1 protein complex containing gamma-actin and non-muscle myosin IIB by analysis of protein-protein interactions.

Identification of an FHL1 protein complex containing gamma-actin and non-muscle myosin IIB by analysis of protein-protein interactions.

... interacting protein bands with approximate molecular weights of 220 kDa, 50 kDa and 40 kDa ...IPI protein sequence database, and only those proteins, which were supported by at least two unique peptides per ... See full document

8

Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery.

Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery.

... their protein-protein interactions can evoke latent DNA specificities, causing them to occupy binding sites rarely bound by the isolated protein ... See full document

23

A flow cytometry-based FRET assay to identify and analyse protein-protein interactions in living cells.

A flow cytometry-based FRET assay to identify and analyse protein-protein interactions in living cells.

... by using the single cutter restriction sites NheI and ...by using the unique XhoI and EcoRI sites and amplification of the target with 59pXhoI-CGCTCGAGCT- (target sequence) and 39-EcoRI-CTGAATTC-(target ... See full document

10

Recognition of anesthetic barbiturates by a protein binding site: a high resolution structural analysis.

Recognition of anesthetic barbiturates by a protein binding site: a high resolution structural analysis.

... Within the barbiturate class, different compounds potentiate GABA effects and mediate anesthesia with different potencies; these differences are largely mirrored in their affinities for apoferritin. It is therefore ... See full document

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