novel fold and ab initio methods for protein structure generation

... structures in segment assembly based methods) Doing so improves the efficiency of folding simulation and ab initio methods for protein structure prediction 1.2.3.2 Reduced Models of Proteins and ... loop structures: knowledge-based methods and ab initio methods Knowledge-based methods build the loop structures using the known structures of loops from all proteins in the structure database, ... approaches (Samudrala et al., 1999) 1.2.3.1 Protein Folding Simulation and ab Initio Structure Prediction Protein folding simulation and protein tertiary structure prediction are two distinct yet...

Ngày tải lên: 27/06/2014, 10:20

Ngày tải lên: 08/03/2014, 05:21

... the loudness expressing its importance, and pointing at a wall and repeatedly firing the gun to project information about each appointment Note Designing for extreme characters is a technique which ... one hand, he shows of how busy he is, enforcing his position On the other, he does not want to disclose any details about his appointments The rings form a kind of augmented ‘knot-in-a-handkerchief’ ... stereotypical, and to at least one reviewer offensively so The jewellery wearing drugsdealer and the attractive polyandrous woman touch upon sensitive issues such as race and gender, and the clichéd...

Ngày tải lên: 16/03/2014, 18:20

... 35.4°, compared to 35.7° for the native 10mer, 35.2° for 10-DAPI and 35.6° for 10-Dst, ˚ ˚ ˚ ˚ and a helical rise of 3.29 A (3.27 A, 3.32 A and 3.25 A for the 10mer, 10-DAPI and 10-Dst, respectively), ... pyrrole rings A and B, between the guanidinium end and pyrrole ring A, and between the amidinium end and pyrrole ring B for the 10-Nt reported structure, NETRSN [31] structure and the DFT approximation ... factor is 42.9, 37.2 and ˚ 27.9 A2 for phosphate groups (including O5¢ and O3¢), sugars (excluding O5¢ and O3¢) and bases, respectively The overall temperature factor for the whole structure ˚ (including...

Ngày tải lên: 16/03/2014, 22:20

... relations for Information Extraction (IE) and QA, as in (Riloff and Shepherd, 1997; Ravichandran and Hovy, 2002; Yangarber et al., 2000) Patterns identify rather specific and informative structures ... entailment acquisition based on (Hearst, 1992) and (Pantel et al., 2004) Capitalized terms indicate variables pl and sg stand for plural and singular forms relation are found based on a set of manually ... Acquiring candidate entailment pairs for the input term by pattern-based and distributional similarity methods (Section 3.2); 2: Constructing a feature set for all candidates based on pattern-based and...

Ngày tải lên: 17/03/2014, 04:20

... in GIS and SCGIS Hence each Newton direction needs O(¯ l) We summarize the cost for solving sub-problems in Table Comparison and a New CD Method 3.1 Comparison of IS/CD methods From the above ... (POS) tagging for BROWN corpus (http://www.nltk.org) and chunking tasks for CoNLL2000 (http://www cnts.ua.ac.be/conll2000/chunking) We randomly split the BROWN corpus to 4/5 training and 1/5 testing ... all Sw(x, y) and Tw(x) This trick for updating Pw(y|x) has been used in SCGIS (Goodman, 2002) Thus, the first Newton iteration of all methods discussed here takes O(¯ operations For each subsequent...

Ngày tải lên: 23/03/2014, 17:20

... parameters compared to known methods, which are based on word trigrams This method also has the advantage that training can be done once and for all, and quite manageably, for all confusion sets; ... (Golding and Roth, 1996) We adopt the Bayesian hybrid method, which we will call Bayes, having experimented with each of the methods and found Bayes to be among the best-performing for the task at hand ... negatives and increasing false positives The results of Word and Tribayes for the 18 confusion sets appear in Table Six of the confusion sets (marked with asterisks in the table) are not handled...

Ngày tải lên: 23/03/2014, 20:21

... observed and calculated values of log kf for selected models (a and b) c=nðÞ; c=n and ÁG=n (&); and c=n; ÁG=n and pe ð4Þ (c and d) c=nðÞ; c=n and nc (&); and c=n; nc ; and ÁGð4Þ (a and c) Training ... Friesner 223 Deterministic Global Optimization and Ab Initio Approaches for the Structure Prediction of Polypeptides, Dynamics of Protein Folding, and Protein Protein Interactions By John L Klepeis, ... predict protein structure via simulation, without direct reference to structures in the PDB, this is referred to as ‘ ab initio protein ’ structure prediction Potential energy functions for ab initio...

Ngày tải lên: 11/04/2014, 01:33

... employed and X1n (f) and X2n (f) are the discrete Fourier transforms of the nth data segments of x1 (t) and x2 (t) This estimate is biased and its probability density function for non-weighted and ... the estimate and is therefore 2π periodic and would thus yield the same result for integer multiples of delay For significant coherence present over a band of frequencies, Mima and colleagues ... coherence plot computed for the spike trains of two MU's and the associated 95% confidence level The coherence plots reveal the bandwidth and values of significant coherence for the given resolution...

Ngày tải lên: 19/06/2014, 10:20

... data-adaptive amplitude and phase estimation (APES) [9, 10] methods have been considered for image formation For multistatic ultra-wideband CMI, the DAS- [11] and RCB-based adaptive [16] methods have been ... breast skin, nipple, and so forth Signal processing algorithms can be classified as datadependent (data-adaptive) and data-independent methods For mono- and bistatic ultra-wideband CMI, the simple ... only, ˇ and Ii, j (t) is due to the interference from breast skin, nipple, and so forth (without tumor response), both of which are not available in practice To compute SNR and SINR, we performed...

Ngày tải lên: 22/06/2014, 23:20

... in table 6, truncation points of - to + and step length of These for dimensions to truncation points are identical for each variable The correlation value between variables depends on n and is ... will assume that the variables are separated into mutually independent blocks of variables Tables and respectively outline the results obtained for and dimensions when absolute values of non-zero ... integral, in cases for which this value could be computed a priori The results in table 6, for dimensions and with different correlation matrices the used in table and one of those used in table empirically...

Ngày tải lên: 09/08/2014, 22:22

... of variables to predict the variable of interest The formula for three variables is r1.23 ϭ 2 r12 ϩ r13 Ϫ 2r12 r13r23 1Ϫ r23 (32) Generalizations are available for larger numbers of variables ... value for the population parameter, which is known as the Most Probable Number (MPN) (Fair and Geyer, 1954) Tables have been prepared for estimating the MPN for such tests on this principle, and ... correlation formula for three variables is r12.3 ϭ r12 Ϫ r13r23 2 1Ϫ r13 1Ϫ r23 , (33) where r12.3 gives the correlation of variables and 2, with the contribution of variable held constant This formula...

Ngày tải lên: 10/08/2014, 20:20

... detect, visualize and analyze residue co-locations in and between protein structures [14] Eighty different protein structures were taken from the protein structure database [15] and residue co-locations ... Theoretical Biology and Medical Modelling 2006, 3:15 modeling; (2) fold recognition; and (3) ab initio methods The first two methods are knowledge based (database-driven), i.e some template ... step of ab initio protein structure prediction (as well as protein design) is the prediction of the secondary structure (i.e the location and length of alpha helices, beta strands and turns)...

Ngày tải lên: 13/08/2014, 23:20

... 42 viii ABSTRACT Joshi, Abhishek Shriram M.S., Purdue University, August, 2012 Image Processing and Super Resolution Methods for a Linear 3D Range Image Scanning Device for Forensic Imaging ... Zheng for agreeing to be a part of my Thesis Committee Thank you to all my friends and well-wishers for their good wishes and support And most importantly, I would like to thank my family for their ... http://www.purdue.edu/policies/pages/teach_res_outreach/c_22.html IMAGE PROCESSING AND SUPER RESOLUTION METHODS FOR A LINEAR 3D RANGE IMAGE SCANNING DEVICE FOR FORENSIC IMAGING  A Thesis Submitted to the Faculty of Purdue University by Abhishek Shriram Joshi...

Ngày tải lên: 24/08/2014, 10:38

... Phoebe for always being there for me and for having absolute confidence in me They have been the greatest source of strength and support in my work and in my life ii Table of Contents Acknowledgements ... different metrics and functional similarity for different sets of interaction neighbors 30  Table 2-4 Estimated reliability for each experimental source in the GRID protein- protein interactions ... tertiary structure [18, 19, 20], and gene expression profiles [21] Sequence homology offers a quick and effective way of suggesting possible functions for novel proteins, but its applicability...

Ngày tải lên: 12/09/2015, 08:18

... Devices Using Ab Initio Methods Zou Xu (B Eng., University of Science and Technology of China, P R China) A THESIS SUBMITTED FOR THE DEGREE OF MASTER OF ENGINEERING DEPARTMENT OF ELECTRICAL AND COMPUTER ... Singapore, Prof Wang Qing Guo, for his invaluable suggestions and help on my academic and research matters I want to thank Dr Liu En Feng for his contribution and support throughout programming ... experiments However, to fully understand the electron transport mechanism of the device, exact modeling and simulation method is needed 1.3 Ab Initio Methods for Molecular Electronic Device Simulation...

Ngày tải lên: 05/10/2015, 19:03

... that: (i) Cn and F are closed and convex subset of C for all n ≥ Therefore, ΠCn x0 , n ≥ and Π F x0 are well-defined (ii) F ⊂ Cn for all n ≥ Suppose F ⊂ Cn for some n ≥ (F ⊂ C0 = C) For each u ... 18 March 2014 © Korean Society for Computational and Applied Mathematics 2014 Abstract In this paper we study some novel parallel and sequential hybrid methods for finding a common fixed point ... , and Jr = (J + r A)−1 J : E → D(A) be the resolvent of A with r > Then, (i) F(Jr ) = A−1 0; (ii) φ(u, Jr x) ≤ φ(u, x) for all u ∈ A−1 and x ∈ E Lemma [26] Let E be a uniformly convex and uniformly...

Ngày tải lên: 14/10/2015, 08:19

... therefore applied to Soil -Structure- Fluid Interaction in arch dams and sheet-piles, SoilStructure Interaction for a nuclear reactor resting on a layered half-space with random heterogeneities and ... connected to the ground and the interaction between the artefact and the foundation medium may affect considerably both the superstructure and the foundation soil The Soil -Structure Interaction ... Boundary Element Methods for Soil -Structure Interaction This page intentionally left blank Boundary Element Methods for Soil -Structure Interaction Edited by W.S HALL University...

Ngày tải lên: 17/08/2013, 11:30

... for GSM and FEM are essentially the same 2) The standard FDM works well usually for structured meshes The GSM, however, works well also for unstructured mesh with irregular triangular cells and ... a family of weakened-weak (W2) form methods and weak-form like methods have been recently proposed by Liu et al [16, 17, 51, 63, 64] for solving both the solid and fluid flows problems via applying ... ES-FEM-T3 for FSI analysis From the review above it can be seen that the ES-FEM-T3 and GSM possess interesting characteristics and can perform better than the other smoothed and conventional methods...

Ngày tải lên: 09/09/2015, 10:06

... for Eqns (29) and (30) ext 0;ext ext and 0.1 for Eqns (31) and (32)], and the corresponding slopes are quite close to [1.00 for Eqns (29) and (30); 0.96 and 1.03 for Eqns (31) and (32)] In Tables ... indices for the example protein (Tables and 3) is shown in Table Any local protein bilinear index has a particular meaning, especially for the rst values of k, where the information about the structure ... (34) and (35) and experimental DDGfo for the training and test databases are shown Analysis of the importance of protein structural information for the numerical characterization of Arc mutants and...

Ngày tải lên: 29/03/2014, 09:20