computational methods to predict therapeutic protein aggregation

... proteins belonging to transient complexes This approach is based on two observations Firstly, protein- protein interactions are more easily identified if the interacting protein pair belongs to ... also displayed Cytoskeleton or Cytoplasm GO annotation (Additional data file 8); of these genes are known interactors of PAK1 [29-33], are similar to actin or actin-binding proteins, are tubulins ... analysis of protein complexes Nature 2002, 415:141-147 Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome Proc...

Ngày tải lên: 14/08/2014, 08:20

... and the top PSI-BLAST hit(s) from our database are shown Seven novel candidate selenoproteins are shown in bold type *Each entry corresponds to a computationally identified readthrough protein ... information *Each entry corresponds to a computationally identified read-through protein in the organism indicated to the left FASTA files for these recoded protein sequences are provided in the ... because it can be a selenoprotein itself The RSA method was applied to all the predicted theoretical ORFs (length ≥ 90 residues) that contain an in-frame UGA stop codon Out of a total 203,339 ORFs analyzed,...

Ngày tải lên: 14/08/2014, 14:22

... details 2.2.1) 1.1.2 Protein complex and predicting protein complexes from PPI networks Many proteins have to perform their functions together with other proteins to form protein complexes which ... is to build a complete map of protein -to- protein physical interactions, which is called the interactome Protein- protein interaction network (PPI network) is a mathematical model of the interactome ... eukaryotic interactomes that were studied Figure 1.1 – (a) protein- protein interaction, (b) protein- protein interaction network As efforts to get a complete image of the interactome, many high-throughput...

Ngày tải lên: 01/10/2015, 17:27

... details 2.2.1) 1.1.2 Protein complex and predicting protein complexes from PPI networks Many proteins have to perform their functions together with other proteins to form protein complexes which ... is to build a complete map of protein -to- protein physical interactions, which is called the interactome Protein- protein interaction network (PPI network) is a mathematical model of the interactome ... eukaryotic interactomes that were studied Figure 1.1 – (a) protein- protein interaction, (b) protein- protein interaction network As efforts to get a complete image of the interactome, many high-throughput...

Ngày tải lên: 03/10/2015, 21:56

... details 2.2.1) 1.1.2 Protein complex and predicting protein complexes from PPI networks Many proteins have to perform their functions together with other proteins to form protein complexes which ... is to build a complete map of protein -to- protein physical interactions, which is called the interactome Protein- protein interaction network (PPI network) is a mathematical model of the interactome ... eukaryotic interactomes that were studied Figure 1.1 – (a) protein- protein interaction, (b) protein- protein interaction network As efforts to get a complete image of the interactome, many high-throughput...

Ngày tải lên: 04/10/2015, 07:57

Ngày tải lên: 19/02/2014, 03:20

... GPCR : G protein stoichiometry of the fusion proteins allowing the G protein fused to one receptor to interact with the G protein of another receptor-G protein fusion that may or may not be part ... fluorescent protein (GFP) from Victoria aequoria has found widespread use in cell biology to monitor the expression and distribution of proteins tagged with this polypeptide Mutation of this protein ... A G protein- coupled receptors function via agonist-mediated trans-activation of associated G proteins J Biol Chem 278, 42578–42587 62 Milligan G (2002) The use of receptor-G protein fusion proteins...

Ngày tải lên: 16/03/2014, 22:20

... Computer Methods, Nicholas Copernicus University, Torun, Poland Heather D Schafroth, Department of Chemical Engineering, Princeton University, Princeton, NJ, U.S.A Jeffrey Skolnick, Laboratory of Computational ... insight into the general thermodynamic and kinetic issues as to why and how proteins fold into a unique native state; they can also be profitably used to model folding kinetics, as well as to make ... insights into the basis of protein folding and results for modeling of specific protein folding events Reduced models of proteins (i.e., models not containing complete atomic detail) can be used to make...

Ngày tải lên: 11/04/2014, 01:33

... various tools in CASP is described Chapter 14 (Structure Prediction of Membrane Proteins) covers the methods for prediction of secondary structure and topology of membrane proteins, as well as prediction ... for Computational Studies of Proteins) discusses the theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein protein ... resources for membrane protein structure prediction is also provided Chapter 15 (Structure Prediction of Protein Complexes) describes computational issues for docking, including protein protein docking...

Ngày tải lên: 27/06/2014, 10:20

... (0.8 to 1.5) 0.69 1.1 (0.7 to 1.7) 0.66 HAQ 1.9 (1.1 to 3.4) 0.03 2.5 (1.3 to 5.0) 0.01 1.5 (0.6 to 3.7) 0.41 ESR (> 20 mm/h) 5.2 (2.4 to 11.1) < 0.001 5.5 (2.2 to 13.7) < 0.001 4.6 (1.2 to 17.0) ... (1.3 to 8.5) 0.01 2.2 (0.6 to 8.3) 0.23 IgM RF (> 25 U/ml) 1.7 (0.8 to 3.3) 0.14 3.4 (1.5 to 7.8) 0.005 3.8 (1.0 to 14.2) 0.05 DMARD use 2.1 (1.0 to 4.3) 0.05 2.9 (1.3 to 6.3) 0.009 2.5 (0.8 to ... (-8.0 to -3.0) < 0.001 DMARD treatment -1.6 (-2.6 to -0.5) 0.003 -2.6 (-4.3 to -0.9) 0.004 -5.0 (-7.9 to -2.2) 0.001 Prednisolone use -1.0 (-2.2 to 0.1) 0.07 -1.9 (-3.5 to -0.4) 0.02 -3.6 (-6.2 to...

Ngày tải lên: 09/08/2014, 14:22

... performed to examine the association between mortality and each of the predictors separately We also conducted a forward stepwise multivariate logistic regression to determine the independent predictors ... of the most common models used to evaluate ICU patients’ condition and predict their outcomes [23] The additive ability of NT-proBNP and CRP to APACHE-II score to predict ICU mortality has rarely ... about the predictive value of CRP for short-term mortality [21,22] In addition, although NT-proBNP and CRP have been shown to be predictors of adverse outcomes in ICU patients, the predictive...

Ngày tải lên: 14/08/2014, 07:21

... example, to compare single predictors to random pairs, the expected frequency of phenotype/disease pairs was that of random pairs To compare intersections of predictors to single predictors, the ... applied to identify the best predictor(s) of genetic interactions in yeast These predictor(s) could then be used to predict epistatic interactions that are thought to be responsible for many complex ... studying phenotypes to find what types of data are predictive of phenotypes in yeast; we then apply this framework to human disease phenotypes Results Protein complexes as predictors of phenotype...

Ngày tải lên: 14/08/2014, 08:20

... disorder predictor design At the same time, disorder predictors can give feedback to experimental protocols for accurate identification of intrinsic disorder Among the published disorder predictors, ... disorder prediction and CLADIST classification program to predict structural domains and intrinsically disordered regions GSmetaDisorder is a meta predictor that combines 12 disorder predictors: ... of two methods: Charge/hydropathy and CDFALL It is able to predict proteins into four categories: structured, mixed, disordered and rare SPINE-D is based on a single neural network to predict...

Ngày tải lên: 09/09/2015, 10:14

... are used to describe protein site [11] There are two main groups of methods for predicting protein- protein interaction sites, the methods using protein structure and the methods using protein ... [11], while computational methods are more cost-effective Predicting protein- protein interaction sites by machine learning methods can be dealt as a classification problem that to predict whether ... and to predict which proteins interact with which others The first problem is called protein- protein interaction sites prediction Learning about this issue leads to the understanding how proteins...

Ngày tải lên: 20/05/2016, 16:03

... apoptosis and special growth factors like steroid receptors, human epidermal growth factor receptor, vascular endothelial growth factor and P-glycoprotein [69, 70] Thus nuclear medicine methods, ... factors, i.e their cell receptors as cancer biomarkers to develop new targeted anticancer drugs with better tumor response However, tumor concentrations of growth factor receptors not reliably predict ... cell culture tests As early as the 1950s, research teams started to develop laboratory tests in order to predict tumor reaction to cytostatic drugs [5] They used fresh cancer tissue and examined...

Ngày tải lên: 25/10/2012, 11:10

... therapy are important factors to conduct the monitoring and to understand the data on the serum concentration of digoxin [16-19] The serum level of Cr has been used to estimate the renal function, ... narrow therapeutic range, necessitating the routine monitoring of its serum concentration to maximize the therapeutic effects and minimize toxicities [16-19] Since digoxin is mainly eliminated ... measurement Kidney Int 2004; 65(4):1416–1421 Shimizu-Tokiwa A, Kobata M, Io H, Kobayashi N, Shou I, Funabiki K, Fukui M, Horikoshi S, Shirato I, Saito K, Tomino Y Serum cystatin C is a more sensitive...

Ngày tải lên: 31/10/2012, 17:08

... dương tính hoàn to n tất mẫu kháng huyết thử Điều có nghóa protein tái tổ hợp MBP-VT2eB gây kích ứng miễn dòch thỏ tạo kháng thể đặc hiệu protein tái tổ hợp MBP-VT2eB Tuy nhiên protein tái tổ ... protein tái tổ hợp MBP-VT2eB Tuy nhiên protein tái tổ hợp cấu tạo thành phần: protein dung hợp MBP (Maltose Binding Protein) protein tiểu phần B độc tố VT2e nên không loại trừ khả kết dương tính thu ... 1, 2, 3, 4, 5, chứa 10 µl protein MBPVT2eB pha loãng từ nồng độ ban đầu đến nồng độ 1/32 Giếng chứa 10 µl kháng huyết Vạch kết tủa kháng thể kháng protein tái tổ hợp protein tái tổ hợp (mũi tên...

Ngày tải lên: 07/04/2013, 20:10

... 0.2% Increasing load to full load causes in-cylinder peak pressure to increase to 50.2 bar from 42.3 bar and ignition delay decreased to 7.9 CAD from 10.7 CAD with respect to 50% load It is clear ... numerical predictions in the case of baseline engine makes the proposed model a reliable tool to be used for exploring new engine concepts 45 50 Experimental model motoring 40 Experimental model motoring ... weaker due to opposing flow in glow plug channel (don’t shown contours) Therefore, at the end of injection period at 380°CA the flame reaches near to injector location without distortion Also...

Ngày tải lên: 05/09/2013, 16:11

... and the DataReader Get* methods that return each C# type You use this table to figure out which method to call to get a specific column type For example, if you need to get the value of a bigint ... Chapter 2, "Introduction to Databases." Note The Get* methods are defined in all of the DataReader classes and work for all databases Next you'll see how to use some of the methods shown in Table ... smallmoney decimal GetDecimal() Table 9.4: SQL SERVER TYPES, COMPATIBLE STANDARD C# TYPES, AND GET* METHODS SQL SERVER TYPE COMPATIBLE STANDARD C# TYPE GET* METHOD sql_varient object GetValue() text...

Ngày tải lên: 24/12/2013, 01:17

... where: r is the tower top radius; r is the tower mid-section radius; r is the tower base radius; h is the height from base to mid-section; h is the height from mid-section to top; Ht = h + h ... Damping resistor applied to an inductance IEC 765/04 Figure – Damping resistor applied to a capacitance It is also possible to apply the backward Euler rule for a few time steps to damp the oscillation ... detail 8.3.3 Computational tools The evaluation of TOV is performed by means of simulation To this end, three kinds of tools are available: – digital computer programmes devoted to time-domain...

Ngày tải lên: 25/12/2013, 10:30