scholarly journals Benchmarking the PEPOP methods for mimicking discontinuous epitopes

2018 ◽  
Author(s):  
Vincent Demolombe ◽  
Alexandre G. de Brevern ◽  
Franck Molina ◽  
Géraldine Lavigne ◽  
Claude Granier ◽  
...  
Keyword(s):  
Protein Antigens ◽  
X Ray Crystallography ◽  
New Methods ◽  
Comparable Method ◽  
Version 2.0 ◽  
Peptide Prediction ◽  
The Traveling Salesman Problem ◽  
Antigen Antibody ◽  
Discontinuous Epitopes ◽  
Better Than

AbstractComputational methods provide approaches to identify epitopes in protein antigens to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was developed as an antigenic or immunogenic peptide prediction tool. We have now improved this tool by implementing 32 new methods (PEPOP version 2.0) to guide the choice of peptides that mimic discontinuous epitopes and thus potentially able to replace the cognate protein antigen in its interaction with an antibody. In the present work, we describe these new methods and the benchmarking of their performances.Benchmarking was carried out by comparing the peptides predicted by the different methods and the corresponding epitopes determined by X-ray crystallography in a dataset of 75 antigen-antibody complexes. The Sensitivity (Se) and Positive Predictive Value (PPV) parameters were used to assess the performance of these methods. The results were compared to that of peptides obtained either by chance or by using the SUPERFICIAL tool, the only available comparable method.The PEPOP methods were more efficient than, or as much as chance, and 33 of the 34 PEPOP methods performed better than SUPERFICIAL. Overall, “optimized” methods (tools that use the traveling salesman problem approach to design peptides) can predict peptides that best match true epitopes in most cases.

scholarly journals Benchmarking the PEPOP methods for mimicking discontinuous epitopes

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Vincent Demolombe ◽  
Alexandre G. de Brevern ◽  
Franck Molina ◽  
Géraldine Lavigne ◽  
Claude Granier ◽  
...  
Keyword(s):  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Comparable Method ◽  
Version 2.0 ◽  
Peptide Prediction ◽  
The Traveling Salesman Problem ◽  
Discontinuous Epitopes ◽  
Cognate Protein ◽  
Better Than

Abstract Background Computational methods provide approaches to identify epitopes in protein Ags to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was developed as an antigenic or immunogenic peptide prediction tool. We have now improved this tool by implementing 32 new methods (PEPOP version 2.0) to guide the choice of peptides that mimic discontinuous epitopes and thus potentially able to replace the cognate protein Ag in its interaction with an Ab. In the present work, we describe these new methods and the benchmarking of their performances. Results Benchmarking was carried out by comparing the peptides predicted by the different methods and the corresponding epitopes determined by X-ray crystallography in a dataset of 75 Ag-Ab complexes. The Sensitivity (Se) and Positive Predictive Value (PPV) parameters were used to assess the performance of these methods. The results were compared to that of peptides obtained either by chance or by using the SUPERFICIAL tool, the only available comparable method. Conclusion The PEPOP methods were more efficient than, or as much as chance, and 33 of the 34 PEPOP methods performed better than SUPERFICIAL. Overall, “optimized” methods (tools that use the traveling salesman problem approach to design peptides) can predict peptides that best match true epitopes in most cases.

scholarly journals PEPOP: new approaches to mimic non-continous epitopes

2018 ◽  
Author(s):  
Vincent Demolombe ◽  
Alexandre de Brevern ◽  
Liza Felicori ◽  
Christophe NGuyen ◽  
Ricardo Andrez Machado de Avila ◽  
...  
Keyword(s):  
Binding Sites ◽  
Web Site ◽  
Peptide Design ◽  
Antigenic Peptides ◽  
New Methods ◽  
Bioinformatics Tools ◽  
Peptide Prediction ◽  
User Friendly ◽  
Discontinuous Epitopes ◽  
Cognate Protein

AbstractBioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits as replacing a protein difficult to produce, or toxic. Using peptides is less expensive. Peptides are easier to manipulate, and can be used as drugs. Continuous epitope predicted by bioinformatics tools are commonly used and these sequential epitopes are used as such in further experiments. Numerous discontinuous epitope predictors have been developed but only two bioinformatics tools proposed so far to predict peptide sequences: Superficial and PEPOP. PEPOP can generate series of peptide sequences that can replace continuous or discontinuous epitopes in their interaction with their cognate antibody. We have developed an improved version of PEPOP dedicated to answer to the experimentalists’ need for a tool able to handle proteins and to turn them into peptides. The PEPOP web site has been reorganized by peptide prediction category and is therefore better formulated to experimental designs. Since the first version of PEPOP, 32 new methods of peptide design were developed. In total, PEPOP proposes 35 methods in which 34 deal specifically with discontinuous epitopes, the most represented epitope type in nature.We present the user-friendly, well-structured web-site of PEPOP and its validation through the use of predicted immunogenic or antigenic peptides mimicking discontinuous epitopes in different experimental ways. PEPOP proposes 35 methods of peptide design to guide experimentalists in using peptides potentially capable of replacing the cognate protein in its interaction with an Ab.

Structural and vibrational studies of 1,1,3,3-tetracyanopropane and 2,2,4,4,6-pentacyanocyclohexenamine

1987 ◽  
Vol 65 (2) ◽  
pp. 261-270 ◽  
Author(s):  
R. A. Bell ◽  
B. E. Brown ◽  
M. Duarte ◽  
H. E. Howard-Lock ◽  
C. J. L. Lock
Keyword(s):  
Unit Cell ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Cell Dimensions ◽  
Cell Data ◽  
Unit Cell Data ◽  
Monoclinic Cell ◽  
C Nmr

1,1,3,3-Tetracyanopropane, 1, was prepared in low yields by a literature method with 2,2,4,4,6-pentacyanocyclohexenamine, 2, as a major by-product. The products were examined by X-ray crystallography. 1 has an orthorhombic space group, Pbcn (No. 60) with cell dimensions, a = 7.158(2), b = 10.510(3), c = 9.733(2) Å and has four formula units in the unit cell. 2 has a monoclinic cell, P21/c (No. 14) with cell dimensions a = 14.368(3), b = 6.626(1), c = 12.300(2) Å, β = 115.60(1)° and has 4 formula units in the unit cell. Data were collected with use of MoKα radiation and a Nicolet P3 diffractometer. The crystal structures were determined by standard methods and refined to Rw = 0.037 (1) and Rw = 0.040 (2) on the basis of 782 and 2108 unique reflections. Bond lengths and angles in the two compounds are normal. 2 has what has been considered to be the less likely tautomeric structure. Both compounds were examined by 1H, 13C nmr, vibrational spectroscopy, and mass spectroscopy. For 2 there was no evidence of the alternative tautomeric structure. New methods were developed for the preparation of both compounds and the mechanism of the original reaction rationalized.

scholarly journals Estimating feedforward and feedback effective connections from fMRI time series: Assessments of statistical methods

2019 ◽  
Vol 3 (2) ◽  
pp. 274-306 ◽  
Author(s):  
Ruben Sanchez-Romero ◽  
Joseph D. Ramsey ◽  
Kun Zhang ◽  
Madelyn R. K. Glymour ◽  
Biwei Huang ◽  
...  
Keyword(s):  
Time Series ◽  
Statistical Methods ◽  
Permutation Test ◽  
Causal Structure ◽  
Multiple Model ◽  
New Methods ◽  
Test Models ◽  
Non Gaussian ◽  
True Structure ◽  
Better Than

We test the adequacies of several proposed and two new statistical methods for recovering the causal structure of systems with feedback from synthetic BOLD time series. We compare an adaptation of the first correct method for recovering cyclic linear systems; Granger causal regression; a multivariate autoregressive model with a permutation test; the Group Iterative Multiple Model Estimation (GIMME) algorithm; the Ramsey et al. non-Gaussian methods; two non-Gaussian methods by Hyvärinen and Smith; a method due to Patel et al.; and the GlobalMIT algorithm. We introduce and also compare two new methods, Fast Adjacency Skewness (FASK) and Two-Step, both of which exploit non-Gaussian features of the BOLD signal. We give theoretical justifications for the latter two algorithms. Our test models include feedback structures with and without direct feedback (2-cycles), excitatory and inhibitory feedback, models using experimentally determined structural connectivities of macaques, and empirical human resting-state and task data. We find that averaged over all of our simulations, including those with 2-cycles, several of these methods have a better than 80% orientation precision (i.e., the probability of a directed edge is in the true structure given that a procedure estimates it to be so) and the two new methods also have better than 80% recall (probability of recovering an orientation in the true structure).

scholarly journals KUALITAS BELANJA DAERAH DAN HUBUNGANNYA DENGAN KINERJA PEMBANGUNAN DI PROVINSI BANTEN

2018 ◽  
Vol 6 (2) ◽  
pp. 16-31
Author(s):  
Sri Wahyuni ◽  
Bambang Juanda ◽  
Idqan Fahmi
Keyword(s):  
Structural Equation ◽  
Secondary Data ◽  
Equation Model ◽  
Version 2.0 ◽  
Performance Development ◽  
And Performance ◽  
The Relationship ◽  
Quality Map ◽  
Better Than

This study aims to analyze the relevant indicators of spending quality in measuring the quality of regional spending as well as the relationship between the quality of regional spending and the development performance of the regencies/cities of Banten Province. This study uses secondary data from the governance, financial and performance development of the districts/cities of Banten Province between 2009 – 2013. The Data are analyzed using Partial Least Squares Structural Equation Model (PLS–SEM) using SmartPLS software version 2.0 & SmartPLS version 3.0. The Results show that there are 21 indicators out of 40 indicators that are relevant in measuring the quality of the districts/cities spending in Banten Province. The change of the spending quality map from 2009 to 2013 shows that the quality of North Banten (Tangerang Regency, Tangerang City, Tangerang Selatan, Serang Regency, Serang City and Cilegon City) is better than South Banten (Pandeglang and Lebak). In addition, the estimation results from the model used indicate that the quality of the region spending of Banten Provinve has a positive relationship with the performance of development with the value of the indicator 0,678. Keywords : Development Performance, PLS-SEM, Spending Quality

LEARNING TO COOPERATE IN SOLVING THE TRAVELING SALESMAN PROBLEM

2005 ◽  
Vol 15 (01n02) ◽  
pp. 151-162 ◽  
Author(s):  
DEHU QI ◽  
RON SUN
Keyword(s):  
Reinforcement Learning ◽  
Traveling Salesman Problem ◽  
Single Agent ◽  
Traveling Salesman ◽  
Cooperative Team ◽  
The Traveling Salesman Problem ◽  
Better Than

A cooperative team of agents may perform many tasks better than single agents. The question is how cooperation among self-interested agents should be achieved. It is important that, while we encourage cooperation among agents in a team, we maintain autonomy of individual agents as much as possible, so as to maintain flexibility and generality. This paper presents an approach based on bidding utilizing reinforcement values acquired through reinforcement learning. We tested and analyzed this approach and demonstrated that a team indeed performed better than the best single agent as well as the average of single agents.

scholarly journals Novel 500-GHz Band Waveguide Stepped Septum-Type Circular Polarizer with a New High-Accuracy and Very Small Waveguide Flange

2020 ◽  
Author(s):  
Yutaka Hasegawa ◽  
Hiroyuki Maezawa ◽  
Hideo Ogawa
Keyword(s):  
High Performance ◽  
High Accuracy ◽  
Circular Polarizer ◽  
New Methods ◽  
Position Errors ◽  
Surface Flatness ◽  
Atmospheric Observations ◽  
Dimensional Errors ◽  
Determination Mechanism ◽  
Better Than

Abstract A new waveguide stepped septum-type circular polarizer (SST-CP) was developed to operate in the 500-GHz band for radio astronomical and planetary atmospheric observations. In a previous study, we developed a practical SST-CP for the 230-GHz band. However, several issues prevent this device being easily scaled down to the 500-GHz band, such as manufacturing dimensional errors and waveguide flange position errors. In this study, we developed a new waveguide flange with a high-accuracy position determination mechanism and a very small size of 10 × 10 mm. We also developed a new fabrication technique to obtain very good flatness for the device’s blank materials by high-accuracy polishing using a resin fixture. Using these new methods, the manufactured 500-GHz band SST-CP achieved a cross-polarization talk level of better than – 30 dB at 465–505 GHz, a device surface flatness of within 3 μm, and also the horizontal positioning error of ± 3 μm. These results indicate that the developed 500-GHz band SST-CP has high performance in the high-frequency band, and thus the new manufacturing methods are effective in the 500-GHz band.

scholarly journals Evolving Evolutionary Algorithms Using Linear Genetic Programming

2005 ◽  
Vol 13 (3) ◽  
pp. 387-410 ◽  
Author(s):  
Mihai Oltean
Keyword(s):  
Evolutionary Algorithms ◽  
Genetic Programming ◽  
Numerical Experiments ◽  
Quadratic Assignment Problem ◽  
Function Optimization ◽  
Traveling Salesman ◽  
Quadratic Assignment ◽  
Linear Genetic Programming ◽  
The Traveling Salesman Problem ◽  
Better Than

A new model for evolving Evolutionary Algorithms is proposed in this paper. The model is based on the Linear Genetic Programming (LGP) technique. Every LGP chromosome encodes an EA which is used for solving a particular problem. Several Evolutionary Algorithms for function optimization, the Traveling Salesman Problem and the Quadratic Assignment Problem are evolved by using the considered model. Numerical experiments show that the evolved Evolutionary Algorithms perform similarly and sometimes even better than standard approaches for several well-known benchmarking problems.

Electron Donor-Acceptor Compounds. Synthesis and Structure of 5-(1,4-Benzoquinone-2-yl)-10,15,20-trialkylporphyrins

1998 ◽  
Vol 53 (9) ◽  
pp. 1021-1030 ◽  
Author(s):  
Steffen Runge ◽  
Mathias O. Senge
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Supramolecular Structure ◽  
Crystal Structure Analysis ◽  
Free Base ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Polymeric Chains ◽  
Donor Acceptor

Abstract A series of 5-(benzoquinone)-10,15,20-trialkylporphyrins was synthesized via cross condensation of the respective aldehydes, 2,5-dimethoxybenzaldehyde and pyrrole followed by demethylation with BBr3 and oxidation with PbO2. This method worked reasonably well for compounds bearing the benzoquinone substituent and butyl, isopropyl, 1 -methylpropyl and 2-ethylpropyl residues (2a-d). The free base porphyrin quinones were converted into the zinc(II) complexes (3a-d) all of which showed remarkable stability for porphyrin quinones. The zinc(II) complex 3c bearing isopropyl residues was investigated by X-ray crystallography and showed a supramolecular structure consisting of polymeric chains facilitated by coordina­tion of a benzoquinone oxygen to a neighboring zinc(II) center. Attempts to synthesize a 5-(benzoquinone)-10,15,20-tris(terr-butylporphyrin) resulted in the formation of a yellow porphomethene (4), which could not be oxidized further. A crystal structure analysis of 4, the first for a free base porphomethene, shows an extremely twisted conformation with syn-orientation of the three tert-butyl groups. The results indicate that new methods will have to be developed for the synthesis of nonplanar porphyrin quinones.

scholarly journals Modeling of cytochrome P450 (Cyt P450, CYP) channels

2011 ◽  
Vol 25 (2) ◽  
pp. 63-87 ◽  
Author(s):  
Christopher K. Jankowski ◽  
Julien B. Chiasson ◽  
Étienne Dako ◽  
Kathy Doucet ◽  
Marc E. Surette ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Direct Method ◽  
Outer Side ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Curved Channels ◽  
Modeling Techniques ◽  
On Line ◽  
Structure Of Proteins

The precise location of a substrate in cytochrome P450 (CYP) governs the orientation of the oxidation position. Such information is generally obtained from biochemical data, but modeling approaches have also been used to explain these locations. We used X-ray data and modeling techniques to distinguish between the series of putative linear or curved channels which lead the substrate from the outer side of the protein to the inner, and then into the heme pocket; these techniques were also used to identify the largest such channels. Two new methods for precisely determining the 3-D structure of proteins using X-ray crystallography were proposed in order to identify these channels: first, the use of both straight and curved channels, and second, the sphere method. These data are compared with Poulos channels, and with Caver (or Mol on line) modeling methodologies. Our methods were developed from studies of the interaction between cytochrome P450CAM(CYP101) fromPseudomonas putida(as expressed inEscherichia coli) and the indolic base β-carboline. Apart from the identification of potential access channels leading to the heme-containing active site, a new explanation was advanced for the substrate's hydroxylation position. The sphere method seems to have potential to become a general and direct method for prediction of substrate access channels from reduced- or low-resolution crystallographic data.

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