Estimating the degree of similarity overlap for structural data in spectral databases

2005 ◽  
Vol 543 (1-2) ◽  
pp. 177-180 ◽  
Author(s):  
T.A. Kornakova ◽  
T.F. Bogdanova ◽  
B.G. Derendyaev ◽  
V.N. Piottukh-Peletsky
Author(s):  
K. H. Downing ◽  
S. G. Wolf ◽  
E. Nogales

Microtubules are involved in a host of critical cell activities, many of which involve transport of organelles through the cell. Different sets of microtubules appear to form during the cell cycle for different functions. Knowledge of the structure of tubulin will be necessary in order to understand the various functional mechanisms of microtubule assemble, disassembly, and interaction with other molecules, but tubulin has so far resisted crystallization for x-ray diffraction studies. Fortuitously, in the presence of zinc ions, tubulin also forms two-dimensional, crystalline sheets that are ideally suited for study by electron microscopy. We have refined procedures for forming the sheets and preparing them for EM, and have been able to obtain high-resolution structural data that sheds light on the formation and stabilization of microtubules, and even the interaction with a therapeutic drug.Tubulin sheets had been extensively studied in negative stain, demonstrating that the same protofilament structure was formed in the sheets and microtubules. For high resolution studies, we have found that the sheets embedded in either glucose or tannin diffract to around 3 Å.


Author(s):  
S. Wang ◽  
P. R. Buseck

Valleriite is an unusual mineral, consisting of intergrowths of sulfide layers (corresponding in structure to the mineral smythite - Fe9S11) and hydroxide layers (corresponding to brucite - Mg(OH2)). It has a composition of approximately 1.526[Mg.68Al.32(OH)2].[Fe1.07Cu.93S2] and consists of two interpenetrating lattices, each of which retains its individual structural and diffraction characteristics parallel to the layering. The valleriite structure is related to that of tochilinite, an unusual iron-rich mineral that is of considerable interest for the origin of certain carbonaceous chondrite meteorites and to those of franckeite and cylindrite, two minerals that are of interest because of their unique morphological and crystallographic properties, e.g., the distinctive curved form of cylindrite and the perfect mica-like cleavage with unusual striations and the long-period wavy structure of franckeite.Our selected-area electron diffraction (SAED) patterns and high-resolution transmission electron microscope (HRTEM) images of valleriite provide new structural data. A basic structure and a new superstructure have been observed.


2002 ◽  
Vol 69 ◽  
pp. 117-134 ◽  
Author(s):  
Stuart M. Haslam ◽  
David Gems ◽  
Howard R. Morris ◽  
Anne Dell

There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fucα1–2Gal1–2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccharomyces cerevisiae and Drosophila melanogaster is also discussed briefly.


2014 ◽  
Vol 6 (1) ◽  
pp. 33-38
Author(s):  
Aditia Rinaldi

Cryptographic hash value has long been used as a database of signatures to identify malware. The most widely used is the MD5 and/or SHA256. In addition, there are fuzzy hashing that slightly different from the traditional hash: length hash value is not fixed and hash value can be used to calculate the degree of similarity of some malware that may still be a variant. This research use ssdeep tool to calculate fuzzy hash. Database signature with fuzzy hash is smaller than SHA256 and larger than MD5. The level of accuracy for the detection of script-based malware variants is greater than the executable-based malware variants. Index Terms—file signature, fuzzy hashing, malware signature, rolling hashing, sha


2014 ◽  
Vol 6 (2) ◽  
pp. 46-51
Author(s):  
Galang Amanda Dwi P. ◽  
Gregorius Edwadr ◽  
Agus Zainal Arifin

Nowadays, a large number of information can not be reached by the reader because of the misclassification of text-based documents. The misclassified data can also make the readers obtain the wrong information. The method which is proposed by this paper is aiming to classify the documents into the correct group.  Each document will have a membership value in several different classes. The method will be used to find the degree of similarity between the two documents is the semantic similarity. In fact, there is no document that doesn’t have a relationship with the other but their relationship might be close to 0. This method calculates the similarity between two documents by taking into account the level of similarity of words and their synonyms. After all inter-document similarity values obtained, a matrix will be created. The matrix is then used as a semi-supervised factor. The output of this method is the value of the membership of each document, which must be one of the greatest membership value for each document which indicates where the documents are grouped. Classification result computed by the method shows a good value which is 90 %. Index Terms - Fuzzy co-clustering, Heuristic, Semantica Similiarity, Semi-supervised learning.


2020 ◽  
Vol 10 (10) ◽  
pp. 3356 ◽  
Author(s):  
Jose J. Valero-Mas ◽  
Francisco J. Castellanos

Within the Pattern Recognition field, two representations are generally considered for encoding the data: statistical codifications, which describe elements as feature vectors, and structural representations, which encode elements as high-level symbolic data structures such as strings, trees or graphs. While the vast majority of classifiers are capable of addressing statistical spaces, only some particular methods are suitable for structural representations. The kNN classifier constitutes one of the scarce examples of algorithms capable of tackling both statistical and structural spaces. This method is based on the computation of the dissimilarity between all the samples of the set, which is the main reason for its high versatility, but in turn, for its low efficiency as well. Prototype Generation is one of the possibilities for palliating this issue. These mechanisms generate a reduced version of the initial dataset by performing data transformation and aggregation processes on the initial collection. Nevertheless, these generation processes are quite dependent on the data representation considered, being not generally well defined for structural data. In this work we present the adaptation of the generation-based reduction algorithm Reduction through Homogeneous Clusters to the case of string data. This algorithm performs the reduction by partitioning the space into class-homogeneous clusters for then generating a representative prototype as the median value of each group. Thus, the main issue to tackle is the retrieval of the median element of a set of strings. Our comprehensive experimentation comparatively assesses the performance of this algorithm in both the statistical and the string-based spaces. Results prove the relevance of our approach by showing a competitive compromise between classification rate and data reduction.


Author(s):  
Markella Konstantinidou ◽  
Zlata Boiarska ◽  
Roberto Butera ◽  
Constantinos G. Neochoritis ◽  
Katarzyna Kurpiewska ◽  
...  
Keyword(s):  

2007 ◽  
Vol 130 (1) ◽  
pp. 111-116 ◽  
Author(s):  
Artem B. Mamonov ◽  
Rob D. Coalson ◽  
Mark L. Zeidel ◽  
John C. Mathai

Determining the mechanisms of flux through protein channels requires a combination of structural data, permeability measurement, and molecular dynamics (MD) simulations. To further clarify the mechanism of flux through aquaporin 1 (AQP1), osmotic pf (cm3/s/pore) and diffusion pd (cm3/s/pore) permeability coefficients per pore of H2O and D2O in AQP1 were calculated using MD simulations. We then compared the simulation results with experimental measurements of the osmotic AQP1 permeabilities of H2O and D2O. In this manner we evaluated the ability of MD simulations to predict actual flux results. For the MD simulations, the force field parameters of the D2O model were reparameterized from the TIP3P water model to reproduce the experimentally observed difference in the bulk self diffusion constants of H2O vs. D2O. Two MD systems (one for each solvent) were constructed, each containing explicit palmitoyl-oleoyl-phosphatidyl-ethanolamine (POPE) phospholipid molecules, solvent, and AQP1. It was found that the calculated value of pf for D2O is ∼15% smaller than for H2O. Bovine AQP1 was reconstituted into palmitoyl-oleoyl-phosphatidylcholine (POPC) liposomes, and it was found that the measured macroscopic osmotic permeability coefficient Pf (cm/s) of D2O is ∼21% lower than for H2O. The combined computational and experimental results suggest that deuterium oxide permeability through AQP1 is similar to that of water. The slightly lower observed osmotic permeability of D2O compared to H2O in AQP1 is most likely due to the lower self diffusion constant of D2O.


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