The Infona portal uses cookies, i.e. strings of text saved by a browser on the user's device. The portal can access those files and use them to remember the user's data, such as their chosen settings (screen view, interface language, etc.), or their login data. By using the Infona portal the user accepts automatic saving and using this information for portal operation purposes. More information on the subject can be found in the Privacy Policy and Terms of Service. By closing this window the user confirms that they have read the information on cookie usage, and they accept the privacy policy and the way cookies are used by the portal. You can change the cookie settings in your browser.
DNA contains information beyond that in its arrangement of A, C, G, T bases. The structure of the DNA (how bases are twisted relative to each other, how deep the grooves between the DNA backbones are, etc.) can have a large impact on vital genomic processes, such as replication, transcription, and nucleosome packaging. It is possible to predict DNA structure from sequence. Databases exist that assign...
In this paper, we describe how neural networks can be used for high throughput screening of potential drug candidates. Individual small molecules (ligands) are assessed for their potential to bind to specific proteins (receptors). Committees of multilayer networks are used to classify protein-ligand complexes as good binders or bad binders, based on selected chemical descriptors. The novel aspects...
The study of proteins and the prediction of their three-dimensional structure is one of the most challenging problem in Structural Bioinformatics. Over the last years, several computational strategies have been proposed as a solution to this problem. As revealed by recent CASP experiments, the best results have been achieved by knowledge-based methods. Despite the advances in the development of computational...
The ability to rapidly identify a given protein from small subsamples (i.e. peptides) is at the basis of fundamental applications in the medical field. At the basis of protein identification we have a string matching problem which is computational intensive if we consider that the complexity of the algorithm scales with the length of the string and the number of sweeps of the database that are needed...
Referring to ab-initio protein structure prediction, a replica exchange based differential evolution searching method (REDE) was proposed. Firstly, employing fragment assembly technique to reduce the dimension of protein conformational space effectively, thus avoiding the entropy effect in searching. Additionally, every replica layer equipped with a conformation population, updating the population...
With the completion of the Human Genome Project, proteomics research has become one of the most important topics in the fields of life science and natural science. The project determined that proteins participate in life activities mainly in the form of complexes. At present, research on protein-protein interaction networks (PPINs) have mainly focused on detecting protein complexes or function modules...
Proteogenomics is an emerging field of systems biology research at the intersection of proteomics and genomics. Two high-throughput technologies, Mass Spectrometry (MS) for proteomics and Next Generation Sequencing (NGS) machines for genomics are required to conduct proteogenomics studies. Independently both MS and NGS technologies are inflicted with data deluge which creates problems of storage,...
To improve the accuracy of prediction of sub-cellular location, a new method using kernel linear discriminant analysis with combinational kernel function which is made up of the Gauss kernel function and the polynomial kernel function is used to the predict the sub-cellular location. In order to confirm the reliability of the research, the data used in this paper are from the standard data set included...
Entire areas of study, such as community phylogenetics and comparative analysis, require detailed phylogenetic, as well as ecological information. China has 31,362 species of vascular plants belonging to 3,328 genera and 312 families, which is ranked in the top six megadiverse countries of the world. along with the big tree of vascular plants in China has been completed recently, SoTree, an automated...
Frequency-based availability analysis for short constituent amino acid sequences provides us with novel possibilities for genome informatics researches specially such as homology search and motif detection. However, it requires very long computation time because of the huge data size and combinatorial explosion. In order to relax the computation time problem, this paper considers the GPU acceleration...
With limited researches, there is still lack of pathway networks of Chuan-wu (also called Aconitum carmichaelii) against rheumatoid arthritis which might provide clues for further researches. In this study, started from the chemical compounds, proteins targeted by Chuan-wu were explored. After that, pathway networks enriched with these targeted proteins were analyzed with hypergeometric distribution...
Frequent subgraph mining is useful in most knowledge discovery tasks such as classification, clustering and indexing. Many algorithms and methods have been developed to mine frequent subgraphs. To have an understanding of several mining frequent subgraph algorithms, it is advantageous to establish a common framework for their study. In this paper, we propose a comparative study of several approaches...
This paper introduces idiom networks of SCS (Short Constituent Sequences) for amino acid sequence analysis, where an idiom represents co-occurrence of two SCSs in a sequence. Thus, the idiom network proposed in this paper shows relations among idioms in an amino acid sequence. The authors also present an idiom network alignment problem, which may useful for protein sequence motif detection and its...
A protein-protein interaction is important for all living cells since it performs important biological functions to form cells as well as control their mechanisms. Identifying PPIs is always a challenge for biology researchers. Many computational methods have been developed to predict PPIs using different data types including gene neighborhood and genetic profiles. However, these methods cannot be...
Sleep-wake cycle is a complex process relates to a variety of neurotransmitters and receptors in the central nervous system (CNS), also involves a large number of gene transcription and translation. MicroRNAs (miRNAs) have emerged as important regulators of gene expression, which mediate translational repression and/or mRNA decay of a target gene. Dopamine D2 receptor (DRD2) gene is predicted as a...
Objective:This study aims to apply closed Non-interactive Literature-Based Knowledge Discovery into the field of traditional Chinese medicine (TCM) to excavate the invisible connection between non-interactive documents and probe into possible hazard factors of the diagnosis and treatment of TCM on Diabetic Retinopathy, thus to offer references for scientific research and clinical scientists. Methods:Non-interactive...
Computational screening of databases have gained immense popularity in the pharmaceutical research and development. To do such screening tests the technique used is Virtual Screening. It uses computer based algorithms and methods which takes into consideration a lot of parameters to discover new ligands on the basis of biological structures. The process of discovering new drugs has now become a crucial...
To accommodate the new features of modern protein mass spectra with Nobel-prize-winner electrospray ionization, Zhixin Tian, et al. developed isotopic Mass-to-charge ratio and Envelope Fingerprinting (iMEF) algorithm for in situ interpretation and database search of protein tandem mass spectra. The creation of the customized theoretical database of both proteins and their dissociated fragment ions...
Network pharmacology has become the new approach for drug mechanism research and novel drug design. Drug target prediction based on computational approach became one of the primary approaches. However, due to the diversity and complexity of herbal chemical structures, the performance of herb target prediction based on chemical structure similarity is limited by the quality and the data availability...
Using graph databases becomes increasingly popular in domains where data can be modeled as a set of connected objects. Graph databases enable to query such data using graphbased queries in a relatively simple manner in comparison to the classical relational databases. In this paper, we show how one of the most popular graph databases, Neo4j, can be applied to the bioinformatics problem of protein-protein...
Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.