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Protein feature extraction
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Kernel-based classification is the current state-of-the-art for extracting pairs of interacting proteins (PPIs) from free text. Various proposals have been put forward, which diverge especially in the specific kernel function, the type of input representation, and the feature sets.
20p
viwyoming2711
16-12-2020
12
0
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A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition
Assigning a protein into one of its folds is a transitional step for discovering three dimensional protein structure, which is a challenging task in bimolecular (biological) science. The present research focuses on: 1) the development of classifiers, and 2) the development of feature extraction techniques based on syntactic and/or physicochemical properties.
11p
viwyoming2711
16-12-2020
16
0
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Amino acid sequences and features extracted from such sequences have been used to predict many protein properties, such as subcellular localization or solubility, using classifier algorithms. Although software tools are available for both feature extraction and classifier construction, their application is not straightforward, requiring users to install various packages and to convert data into different formats.
10p
vikentucky2711
26-11-2020
8
0
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Classifcation of certain proteins with specific functions is momentous for biological research. Encoding approaches of protein sequences for feature extraction play an important role in protein classifcation.
15p
vikentucky2711
24-11-2020
6
1
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Protein-protein interaction (PPI) extraction from published scientific articles is one key issue in biological research due to its importance in grasping biological processes. Despite considerable advances of recent research in automatic PPI extraction from articles, demand remains to enhance the performance of the existing methods.
15p
vioklahoma2711
19-11-2020
17
1
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In this paper, we propose a novel sequence-based approach with multivariate mutual information (MMI) of protein feature representation, for predicting PPIs via Random Forest (RF).
13p
vioklahoma2711
19-11-2020
8
1
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In protein design, correct use of topology is among the initial and most critical feature. Meticulous selection of backbone topology aids in drastically reducing the structure search space. With ProLego, we present a server application to explore the component aspect of protein structures and provide an intuitive and efficient way to scan the protein topology space.
6p
viconnecticut2711
28-10-2020
15
1
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In order to capture the vital structural information of the original protein, the symbol sequence was transformed into the Markov frequency matrix according to the consecutive three residues throughout the chain. A three-dimensional sparse matrix sized 20 × 20 × 20 was obtained and expanded to one-dimensional vector.
10p
viconnecticut2711
28-10-2020
15
2
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Protein feature extraction plays an important role in the areas of similarity analysis of protein sequences and prediction of protein structures, functions and interactions. The feature extraction based on graphical representation is one of the most effective and efficient ways.
10p
vijisoo2711
27-10-2020
23
1
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Although targeted drugs have contributed to impressive advances in the treatment of cancer patients, their clinical benefits on tumor therapies are greatly limited due to intrinsic and acquired resistance of cancer cells against such drugs.
12p
vicolorado2711
23-10-2020
10
0
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Mass spectrometry (MS) has become a promising analytical technique to acquire proteomics information for the characterization of biological samples. Nevertheless, most studies focus on the final proteins identified through a suite of algorithms by using partial MS spectra to compare with the sequence database, while the pattern recognition and classifcation of raw mass-spectrometric data remain unresolved.
15p
vicolorado2711
22-10-2020
20
1
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Apoptosis, also called programmed cell death, refers to the spontaneous and orderly death of cells controlled by genes in order to maintain a stable internal environment. Identifying the subcellular location of apoptosis proteins is very helpful in understanding the mechanism of apoptosis and designing drugs.
19p
vicolorado2711
22-10-2020
26
0
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Kernel based methods dominate the current trend for various relation extraction tasks including protein-protein interaction (PPI) extraction. PPI information is critical in understanding biological processes. Despite considerable efforts, previously reported PPI extraction results show that none of the approaches already known in the literature is consistently better than other approaches when evaluated on different benchmark PPI corpora.
10p
bunthai_1
06-05-2013
46
2
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In this paper we address the problem of extracting features relevant for predicting protein±protein interaction sites from the three-dimensional structures of protein complexes. Our approach is based on information about evolutionary con-servation and surface disposition. We implement a neural network based system, which uses a cross validation proce-dure and allows the correct detection of 73% of the residues involved in protein interactions in a selected database comprising 226 heterodimers.
6p
research12
29-04-2013
29
2
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Searching for bioactive peptides, we analyzed acidic extracts ofPhyllomedusa sauvagiiskin and found two new proteins, PSKP-1 and PSKP-2, of 6.7 and 6.6 kDa, respectively, which, by sequence homology, belong to the Kazal family of serine protease inhibitors. PSKP-1 and PSKP-2 exhibit the unprecedented feature of having proline at P1and P2 positions. A gene encoding PSKP-1 was synthesized and expressed in Escherichia coli. Recombinant PSKP-1 was purified from inclusion bodies, oxidatively refolded to the native state, and characterized by chemical, hydrodynamic andoptical studies. ...
10p
dell39
03-04-2013
38
3
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Analysis of the molecular properties of proteins extracted from organisms living under extreme conditions often highlights peculiar features. We investigated by UV-visible spectroscopy and X-ray crystallography the oxidation pro-cess, promoted by air or ferricyanide, of five hemoglobins extracted from Antarctic fishes (Notothenioidei).
9p
dell39
03-04-2013
28
3
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While the aesthetic and creative process of interior design would best be done by professional interior designers, our goal is to cre- ate software capable of automatically generating furniture arrange- ments for complex indoor scenes that are optimized to respect im- portant ergonomic factors. This technique would be useful in multi- player online games and other graphics applications requiring fully automatic interior design with a high degree of realism.
8p
connhobinh
10-12-2012
63
5
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