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Many proteins and protein regions have been reported to be intrinsically disordered. Such disordered regions have been found to have conformational changes in various biological processes. Comprehensive studies on these disordered regions provide useful clues in understanding the mechanisms of a living cell. However, previous analyses only provided an overall number of disorder residues without definitely...
Most of the existing algorithms for mining frequent patterns could produce lots of projected databases and short patterns which could increase the time and memory cost of mining. In order to overcome such shortcoming, a fast and efficient algorithm named FBPM for mining frequent patterns in biological sequence is proposed. We first present the concept of primary pattern, and then use prefix tree for...
Summary form only given: Viruses have been implicated as the causative agents for a variety of cancers as well as diseases of the major physiological systems (e.g., nervous, respiratory, immune, reproductive, etc.), and viral infections have consistently ranked among the leading causes of death worldwide. Although viruses exhibit extreme biological diversity, plainly evidenced by the Baltimore classification...
The hemagglutinin protein of H3N2 influenza A virus undergoes rapid evolutionary variation that causes many changes in its antigenic epitopes. Because of these changes, annual vaccine formulation needs to be updated to reflect the changes in order to trigger antibodies neutralizing capability. In this paper, the dN/dS ratios of the vaccine strains against the immuno-escape mutant strain circulatings...
In an attempt to enhance the potential based fold - recognition methods of remote homologs, we propose a new approach “Higher Order Residue Interaction Based ALgorithm for Fold REcognition (HORIBALFRE)”, where we incorporated the potential contributions not just from one-body and two-body terms, but from three body (triplet interactions) and four-body (quadruple interaction) interactions, to implement...
The Protein Residue Distance & Angle Distribution Database for Secondary Structures (PRDDs) is a dedicated database and structural bioinformatics system for protein analysis and modeling. The database is developed to host and analyze the statistical data for protein residue level distances and angles (called virtual bonds, bond angles, and torsion angles) obtained from their distributions in databases...
Tandem mass spectrometry is a powerful experimental tool used in molecular biology to determine the composition of protein mixtures. In a tandem mass experiment, peptide ion selection algorithms generally select only the most abundant peptide ions for further fragmentation. Because of this, the low-abundance proteins in a sample rarely get identified. A Real-Time Peptide-Spectrum Matching algorithm...
Prediction of the amino acids that have a catalytic effect on the enzymes is a major stage in appointing the activity of the enzymes and classification. The biological activity of a protein usually depends on the existence of a small number of amino acids. Recently, many algorithms have been proposed in the literature for finding these amino acids which are complex and time consuming. In this paper,...
Similarity search in protein databases is one of the most essential issues in proteomics. With the growing number of experimentally solved protein structures, the focus shifted from sequence to structure. The area of structure similarity forms a big challenge since even no standard definition of optimal similarity exists in the field. In this paper, we propose a protein structure similarity method...
Phylogenomics, conventionally defined as the intersection of phylogenetics and genomics, has become a key instrument in a wide spectrum of biological studies, including resolution of complex evolutionary relationships, assignment of taxonomic affiliation, prediction of protein molecular functions, and tracing horizontal gene transfer event. Here, we introduce an open-source phylogenomic pipeline,...
The protein structure prediction problem is one of the most interesting challenges of computational biology. One of its critical facets is the optimization method employed. This is often carried out by metaheuristics, such as Genetic Algorithms (GA). The prediction involves optimization of a complex and computationally expensive energy function. Thus, the usual GA requirements of a large number of...
The quickly increasing and updating of the protein structure data provides necessary data resources to biological researchers. The use of these data sources needs data integration that is usually time-cost. The data integration should provide a unified data format and deal with synchronization issue. This paper describes an approach for the integration of given protein structure data and its local...
Understanding sequence-structure relationship is the key step in protein modeling and de novo protein design. Although almost 55,000 protein structures are solved and stored in protein data bank, elucidating sequence-structure relationship is still a challenging task. To understand sequence-structure relationship better, a statistical analysis of amino acid residues in four major structural classes...
This paper addresses mutational events that give rise to differing response to drugs focusing on Rac1, a protein that has been recognized as a target for drug design for cardiovascular disease due its regulatory role of angiogenesis. Rac1 has been considered with reference to Single Nucleotide Polymorphism (SNP), which has become of great value for personalized medicine. We have considered four variation...
Analysis of conformational changes is one of the keys to the understanding of protein functions and interactions. For the analysis, we often compare two protein structures, taking flexible regions like hinge regions into consideration. The Root Mean Square Deviation (RMSD) is the most popular measure for comparing two protein structures, but it is only for rigid structures without hinge regions. In...
Protein structure comparison is a important and developing area in Bioinformatics. Understanding the protein structure is very useful, since protein structure suffers less evolutionary changes compared to the amino acid sequences. Thus, comparing protein structures provides additional evolution information. However, structure comparison is not straightforward and multiple algorithms for comparison...
In this study, a QSAR model of neuraminidase (NA) type 1 (Nl) was elevated. This map contained two hydrogen bond acceptor features, one hydrogen bond donor features, and one positive ionizable feature. In the second step, we created the interaction maps in the active sites on the neuraminidase type2, and type7 (N2 and N7) protein structures. The structure-based pharmacophore map was showed the features...
In the protein universe, many proteins are composed of two or more polypeptide chains, generally referred to as subunits, which associate through noncovalent interactions and, occasionally, disulfide bonds. With the number of protein sequences entering into data banks rapidly increasing, we are confronted with a challenge: how to develop an automated method to identify the quaternary attribute for...
Protein function is highly correlated with its three dimensional conformation in order to interact with others proteins, ligands, substrates, inhibitors, etc. Studies on binding site and protein function have been investigated to understand the mechanism of protein activity; therefore, protein stability and flexibility play different roles on protein functions. In this work, we propose a framework...
Expressed sequence tags (ESTs) are single-pass sequence reads from cDNA clones. ESTs usually represent genes expressed in a particular tissue. Single nucleotide polymorphism (SNP) is a very important resource for protein structure and function. It may make a contribution to understand a complex disease, such as tumor. Through analysis of large scale human ESTs, we try to find relationship among SNPs,...
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