computational prediction of human protein interactions

... entire range of protein degrees, an average of 81% of the human proteins are conserved in mice - a number that increases with increasing degree Similarly, on average, 59% of the human proteins are ... expression data with protein- protein interactions Genome Res 2002, 12:37-46 Sprinzak E, Altuvia Y, Margalit H: Colloquium Papers: Characterization and prediction of protein- protein interactions within ... interologous prediction of human interactions from model organisms [10-12], some of which integrated predicted, curated, and experimentally derived interactions [10,13] Analyses of these large...

Ngày tải lên: 14/08/2014, 07:21

... some of those pathway holes This paper describes the generation of HumanCyc, and presents an analysis of the human metabolic map The computationally predicted pathways are consistent with known human ... our understanding of the human metabolic network The query and visualization capabilities of the Pathway Tools software (such as the visual- The user of HumanCyc should be aware of several potential ... more of the 2,709 enzymes in HumanCyc There are more enzymes than reactions because of the existence of isozymes in the human Genome Biology 2004, 6:R2 information The original annotations of the...

Ngày tải lên: 14/08/2014, 14:21

... the presence of a certain function for a protein of interest: (1) number of proteins having this function; (2) number of protein pairs (interacting) having the function; (3) number of protein pairs ... 0 0 0 0 function of a protein The concept of node level was applied to 2559 protein- protein interactions between 6416 proteins collected from the Munich Information center of Protein Sequences ... terms of detecting these weights Conclusions The majority of methods concerning the estimation of protein functions through protein- protein interactions (PPI) use the same weights for all interactions...

Ngày tải lên: 13/08/2014, 16:20

... Superimposition of the solution structure of the human PDI-b¢ (blue) with the crystal structure of yeast PDI-b¢ (red, Protein Data Bank entry code 2B5E) (C) Superimposition of the solution structure of human ... form of the PDI-bb¢ fragment converts into < 10% of dimers in 12 h and < 25% of dimers in days, starting with 0.5 mm of monomers at 30 °C Most of the 1H-15N HSQC signals of the dimeric form of ... coordinate comparison of our solution structure of human PDI-bb¢ and the crystal structure of the I289A mutant of the human PDIb¢x fragment [16] showed differences with an rmsd of ˚ 2.6 A for 116...

Ngày tải lên: 16/03/2014, 04:20

Ngày tải lên: 23/03/2014, 17:20

... of some of the HuMiTar predictions Evaluation and comparison of sensitivity/specificity trade-off based on ROC (receiver operating characteristic) analysis The predictions of HuMiTar on the interactions ... addition of predictions of competing methods to predictions of HuMiTar results in small or no improvement in sensitivity while it increases the total number of predictions; (6) union of the competing ... to provide predictions characterized by favorable sensitivity, which comes at a price of an increased number of predictions The HuMiTar's predictions cover majority of the predictions of the best-performing...

Ngày tải lên: 12/08/2014, 17:20

... interfaces.) Thus, the study of the structural properties of protein protein interfaces, which are responsible for interactions of proteins, can give us a better overview of protein functions, as compared ... characteristics of new proteins, assigning folds to new proteins, analysis of structural variation in protein families, identification of common structural motifs, assessment of sequence alignment ... studied area of clustering protein protein interfaces Any protein rarely acts alone, but rather interacts with other proteins to perform a specific function [NT04] A pair of interacting proteins naturally...

Ngày tải lên: 15/09/2015, 17:10

Ngày tải lên: 15/09/2015, 17:10

... facilities to carry out the research work i Table of Contents Acknowledgement Table of Contents Summary List of Tables List of Figures List of Equations List of Symbols and Abbreviations Chapter Introduction ... applications of SPR biosensors have been developed very fast for the investigation of specific biomolecular interactions including protein- antibody interaction, protein- DNA interaction, protein- cell ... events of thrombin Various target molecules (cofactors and aptamers etc.) have been proved to bind to these exosites and modulate the activity of thrombin [16] Figure 1-1 The ribbon diagram of human...

Ngày tải lên: 03/10/2015, 20:32

... affinity, the ligand binding site of protein, the amino acids of the protein interacting with ligand, PDB files1 of protein bound to ligand etc) of all the 80 lipid -protein interactions are available ... of binding of the ligands of interest to the chosen proteins on the basis of both the characteristics of the binding/active sites and the chemical structure of the ligands” The three groups of ... List of proteins in the bioinformatic component of Lipro Interact 269 Figure 8.8 List of ligands in the bioinformatic component of Lipro Interact 270 Figure 8.9 List of protein- ligand interactions...

Ngày tải lên: 28/11/2015, 14:01

... Functional domains of the capsid ¨ protein of human immunodeficiency virus type J Virol 68, 8180–8187 ˚ ¨ Reicin AS, Ohagen A, Yin L, Hoglund S & Goff SP ¨ (1996) The role of Gag in human immunodeficiency ... analysis of the precise residues and interactions involved in the NTD–CTD interface [46] Most of these involve side chains from helix of the CTD which pack against the N-terminal end of helix of the ... 54 human immunodeficiency virus-1 capsid protein J Mol Biol 318, 519–531 del Alamo M, Neira JL & Mateu MG (2003) Thermodynamic dissection of a low affinity protein- protein interface involved in human...

Ngày tải lên: 18/02/2014, 06:20

... of HIV-1 capsid A Fig Role of TRIM5a and homology model of its PRYSPRY domain (A) The hypothesized role of TRIM5a in the HIV-1 viral life cycle (B) A homology model of the PRYSPRY domain of human ... inhibition of HIV-1 [63,64] More recently, Sebastian et al [65] created a homology model of the PRYSPRY domain of human TRIM5a using the known structures of the same domain from three other proteins ... role of helix of HIV-1 capsid C-terminal domain in interactions with human lysyl-tRNA synthetase J Biol Chem 282, 32274–32279 Fruman DA, Burakoff SJ & Bierer BE (1994) Immunophilins in protein...

Ngày tải lên: 07/03/2014, 00:20

... Discussion Identification of protein complexes by in silico analysis of the expression profiles of human genes In this work, we propose a new method to identify proteinprotein interactions using gene ... Probabilistic model of the human protein- protein interaction network Nat Biotechnol 2005, 23:951-959 Sprinzak E, Altuvia Y, Margalit H: Characterization and prediction of protein- protein interactions ... p value for a subset of the human protein complexes analyzed with PEGO Additional data file is a table listing the number of recovered components for a subset of the human protein complexes analyzed...

Ngày tải lên: 14/08/2014, 08:20

... ecificity Figure Results of protein- protein interaction prediction by PIC Results of protein- protein interaction prediction by PIC (a) Receiver operating characteristic (ROC) curves of PIC for S cerevisiae ... o-localizing protein pairs Figure pairs that co-localize Enrichment of PIC predictions by interacting protein pairs versus protein Enrichment of PIC predictions by interacting protein pairs versus protein ... S cerevisiae is made of protein pairs that not colocalize Therefore, it may be possible that PIC recognizes subcellular localization of proteins instead of protein- protein interactions To examine...

Ngày tải lên: 14/08/2014, 08:21

... composite human protein interaction map, with network properties of each of the datasets Dataset Version Number of interactions Number of proteins Clustering Connectivity < #interactions /protein> ... Visualization of the final consolidated network of protein interactions Visualization of the final consolidated network of protein interactions A view of the composite interaction network (31,609 interactions ... initial list of the interactions and proteins represented in each of the existing human protein interaction datasets with total interactions, unique self -interactions and unique non-self interactions...

Ngày tải lên: 14/08/2014, 14:21

... discussion of computational studies on host-pathogen interactions including: prediction and analysis of host-pathogen protein- protein interactions; basic principles revealed from host-pathogen interactions; ... the degree (in the human interactome) of human proteins involved in H sapiens–EBV PPIs are significantly higher than randomly selected human proteins Thus, these targeted human proteins are enriched ... reachable protein in the network is, on average, smaller than that of randomly-picked human proteins Thus the EBV-targeted human proteins have relatively shorter paths to other proteins in the human...

Ngày tải lên: 10/09/2015, 09:08

... effect of the whole fusion protein in this study We could not determine which part of the fusion protein has this effect The effect might due to either one part of fusion protein or both of them ... function of protein, we designed an enterokinase cleavage site at the 5’ terminus of the gene of the gAd-GLP-1-A fusion protein, which was used to remove the His-tag [9] In our study, most of the ... also proved that majority of fusion protein was present in inclusion body (Fig 2B) Figure Maps of N-terminal His-tagged gAd-GLP-1-A fusion protein and gAd-GLP-1-A fusion protein (A) N-terminal His-tagged...

Ngày tải lên: 25/10/2012, 11:10

... characterized by the lack of hMSH2 protein expression [15] Moreover, Lo Muzio et al [29] reported that 5% of the cases of oral squamous cell carcinoma show diminished expression of hMSH2 protein In the ... errors, the inclusion of cases that had a known history of exposure to recognized carcinogens, and the report of cases of lichenoid dysplasia as malignant transformation of lichen planus Despite ... higher index of cellular proliferation in OLP would require an increased immunolocalization of hMSH2 Therefore, the reduced expression of hMSH2 protein could make the epithelium of OLP more susceptible...

Ngày tải lên: 03/11/2012, 09:54

... further Estimation of cleavage sites in mGFP–calpain Direct interaction between recombinant calpain 7MIT and GST–IST1 proteins The use of cleared lysates of HEK293T cells for all of the experiments ... analysis of tandem MIT domains of calpain and IST1 MIM elements, should clarify these issues in the future Although the physiological role of human calpain is still unknown, the presence of tandem ... Enhancement of calpain autolysis by IST1 Y Osako et al membranes [42] ALIX is recruited to plasma membranes by Gag proteins of HIV-1 and equine infectious anemia virus through binding of the V domain of...

Ngày tải lên: 18/02/2014, 04:20

... during folding of both the CAI peptide and a-helix of CTD during formation of the peptide– protein and protein protein complexes These NMR experiments also allowed the determination of the CTD binding ... the capsid protein of the human immunodeficiency virus type 1: a new drug target? Sci World J 9, 404–419 Mateu MG (2009) The capsid protein of human immunodeficiency virus: intersubunit interactions ... L Neira Gag polyprotein, yields the matrix protein (MA), the capsid protein (CA), the nucleocapsid protein (NC) and p6 proteins, as well as two spacer peptides Currently, most of the available...

Ngày tải lên: 18/02/2014, 06:20