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The Development of a Universal In Silico Predictor of Protein-Protein Interactions  [PDF]
Guilherme T. Valente, Marcio L. Acencio, Cesar Martins, Ney Lemke
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0065587
Abstract: Protein-protein interactions (PPIs) are essential for understanding the function of biological systems and have been characterized using a vast array of experimental techniques. These techniques detect only a small proportion of all PPIs and are labor intensive and time consuming. Therefore, the development of computational methods capable of predicting PPIs accelerates the pace of discovery of new interactions. This paper reports a machine learning-based prediction model, the Universal In Silico Predictor of Protein-Protein Interactions (UNISPPI), which is a decision tree model that can reliably predict PPIs for all species (including proteins from parasite-host associations) using only 20 combinations of amino acids frequencies from interacting and non-interacting proteins as learning features. UNISPPI was able to correctly classify 79.4% and 72.6% of experimentally supported interactions and non-interacting protein pairs, respectively, from an independent test set. Moreover, UNISPPI suggests that the frequencies of the amino acids asparagine, cysteine and isoleucine are important features for distinguishing between interacting and non-interacting protein pairs. We envisage that UNISPPI can be a useful tool for prioritizing interactions for experimental validation.
Computer aided drug design and bioinformatics: A current tool for designing
S. J. Daharwal,Mr. R. B. Saudagar,Mr. Shekh Mohd Azhar
Pharmaceutical Reviews , 2006,
Abstract: Drug design is an integrated developing discipline. It involves the studyof effects of biologically active compound on the basis of molecular interactionin terms of molecular structure or its physiochemical properties involved. The development of new methods in the field of molecular biology and computerscience, has improved the tools for drug design significantly. More and morenew drugs are developed with the help of computer technique.The field of bioinformatics has become a major part of the drug design thatplays a key role for validation drug targets. Bioinformatics can help in understandingof complex biological processes and help improve in understanding of complexbiological processes and help improve drug discovery.KEY WORDS: CADD and Bioinformatics, Tool for designing of drug.
Bioinformatics Resources for In Silico Proteome Analysis
Manuela Pruess,Rolf Apweiler
Journal of Biomedicine and Biotechnology , 2003, DOI: 10.1155/s1110724303209219
Abstract: In the growing field of proteomics, tools for the in silico analysis of proteins and even of whole proteomes are of crucial importance to make best use of the accumulating amount of data. To utilise this data for healthcare and drug development, first the characteristics of proteomes of entire species—mainly the human—have to be understood, before secondly differentiation between individuals can be surveyed. Specialised databases about nucleic acid sequences, protein sequences, protein tertiary structure, genome analysis, and proteome analysis represent useful resources for analysis, characterisation, and classification of protein sequences. Different from most proteomics tools focusing on similarity searches, structure analysis and prediction, detection of specific regions, alignments, data mining, 2D PAGE analysis, or protein modelling, respectively, comprehensive databases like the proteome analysis database benefit from the information stored in different databases and make use of different protein analysis tools to provide computational analysis of whole proteomes.
Bioinformatics Resources for In Silico Proteome Analysis  [cached]
Pruess Manuela,Apweiler Rolf
Journal of Biomedicine and Biotechnology , 2003,
Abstract: In the growing field of proteomics, tools for the in silico analysis of proteins and even of whole proteomes are of crucial importance to make best use of the accumulating amount of data. To utilise this data for healthcare and drug development, first the characteristics of proteomes of entire species mainly the human have to be understood, before secondly differentiation between individuals can be surveyed. Specialised databases about nucleic acid sequences, protein sequences, protein tertiary structure, genome analysis, and proteome analysis represent useful resources for analysis, characterisation, and classification of protein sequences. Different from most proteomics tools focusing on similarity searches, structure analysis and prediction, detection of specific regions, alignments, data mining, 2D PAGE analysis, or protein modelling, respectively, comprehensive databases like the proteome analysis database benefit from the information stored in different databases and make use of different protein analysis tools to provide computational analysis of whole proteomes.
De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes  [PDF]
Christopher A. Gulvik, T. Chad Effler, Steven W. Wilhelm, Alison Buchan
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050362
Abstract: Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (i.e., degeneracies). Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an in silico amplification using user defined nucleotide sequence dataset(s) and primer sequences that may contain degenerate bases. The program returns an output file that contains the in silico amplicons. When De-MetaST is paired with NCBI’s BLAST (De-MetaST-BLAST), the program also returns the top 10 nr NCBI database hits for each recovered in silico amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases, this search tool has potential utility in many data mining applications.
DEVELOPMENT AND IMPLEMENTATION OF A BIOINFORMATICS ONLINE DISTANCE EDUCATION LEARNING TOOL IN AFRICA
Oluwagbemi Olugbenga OLUSEUN
The Turkish Online Journal of Distance Education , 2009,
Abstract: New scientific research fields are evolving on a yearly basis but some parts of the African continent are less aware. Thus, there arises the need for a suitable implementation strategy in introducing the basic components of an emerging scientific field to some part of the African populace through the development of an online distance education learning tool. This emerging field is known as bioinformatics. This research work was instrumental in elucidating the need for a suitable implementation platform for bioinformatics education in parts of the African continent that are less aware of this innovative and interesting field. The aim of this research work was to disseminate the basic knowledge and applications of bioinformatics to these parts of the African continent.
Comprehensive Analysis of rsSNPs Associated with Hypertension Using In-Silico Bioinformatics Tools
Alsadig Gassoum, Nahla E. Abdelraheem, Nehad Elsadig
Open Access Library Journal (OALib Journal) , 2016, DOI: 10.4236/oalib.1102839
Abstract:
Genetic epidemiological studies have suggested that several genetic variants increase the risk for hypertension. It is likely that a number of genes rather than a single gene account for the heritability of this complex disorder. However, the genetic analysis of hypertension produced complex, inconsistent and nonreproducible results, which makes it difficult to draw conclusions about the association between specific genes and hypertension. Material and methods: In this study, we aimed to analyze SNPs that had been investigated in hypertension. These SNPs were collected from text-mind hypertension, obesity and diabetic (T-HOD) data base program, during the period of 31 may 2016. SNPs lists which were reported with hypertension were collected in excel file sheet and processed for analysis using different types of bioinformatics tools and programs. Results: SNPs were evaluated for their deleterious effect on the protein function and stability, in the present study, 7 SNPs were predicted deleterious (A288S, M731T, R172C, R50Q, G460W, K197N, G75V). Mutation3D server showed 3 of mutations (STEA4, PLD2, AZIN2, rs28933400, rs2286672, rs16835244 genes and corresponding rsSNPs respectively) were found to increase risk to hypertension.
Cloud computing and validation of expandable in silico livers
Glen EP Ropella, C Anthony Hunt
BMC Systems Biology , 2010, DOI: 10.1186/1752-0509-4-168
Abstract: The local cluster technology was duplicated in the Amazon EC2 cloud platform. Synthetic modeling protocols were followed to identify a successful parameterization. Experiment sample sizes (number of simulated lobules) on both platforms were 49, 70, 84, and 152 (cloud only). Experimental indistinguishability was demonstrated for ISL outflow profiles of diltiazem using both platforms for experiments consisting of 84 or more samples. The process was analogous to demonstration of results equivalency from two different wet-labs.The results provide additional evidence that disposition simulations using ISLs can cover the behavior space of liver experiments in distinct experimental contexts (there is in silico-to-wet-lab phenotype similarity). The scientific value of experimenting with multiscale biomedical models has been limited to research groups with access to computer clusters. The availability of cloud technology coupled with the evidence of scientific equivalency has lowered the barrier and will greatly facilitate model sharing as well as provide straightforward tools for scaling simulations to encompass greater detail with no extra investment in hardware.The scientific value of multilevel, multiscale, computational, biomedical models will be greatly enhanced by making them broadly available and sufficiently manipulable to address a variety of scientific questions at reasonable costs, regardless of the hardware at the researcher's disposal. The availability of cloud technology opens the door to that eventuality. However, such models are analogous to an entire, specialized, wet laboratory. As with wet laboratories, insuring scientific equivalency of duplicate experimental systems in different laboratories is a necessary precondition for placing confidence in the results of experiments arising from those laboratories. A goal of this project was to test the scientific equivalence of experiments conducted using multilevel, multiscale, In Silico Livers (ISLs) executed on
Developing a powerful In Silico tool for the discovery of novel caspase-3 substrates: a preliminary screening of the human proteome
Muneef Ayyash, Hashem Tamimi, Yaqoub Ashhab
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-14
Abstract: Here, we describe a powerful bioinformatics tool that can predict the presence of caspase-3 cleavage sites in a given protein sequence using a Position-Specific Scoring Matrix (PSSM) approach. The present tool, which we call CAT3, was built using 227 confirmed caspase-3 substrates that were carefully extracted from the literature. Assessing prediction accuracy using 10 fold cross validation, our method shows AUC (area under the ROC curve) of 0.94, sensitivity of 88.83%, and specificity of 89.50%. The ability of CAT3 in predicting the precise cleavage site was demonstrated in comparison to existing state-of-the-art tools. In contrast to other tools which were trained on cleavage sites of various caspases as well as other similar proteases, CAT3 showed a significant decrease in the false positive rate. This cost effective and powerful feature makes CAT3 an ideal tool for high-throughput screening to identify novel caspase-3 substrates.The developed tool, CAT3, was used to screen 13,066 human proteins with assigned gene ontology terms. The analyses revealed the presence of many potential caspase-3 substrates that are not yet described. The majority of these proteins are involved in signal transduction, regulation of cell adhesion, cytoskeleton organization, integrity of the nucleus, and development of nerve cells.CAT3 is a powerful tool that is a clear improvement over existing similar tools, especially in reducing the false positive rate. Human proteome screening, using CAT3, indicate the presence of a large number of possible caspase-3 substrates that exceed the anticipated figure. In addition to their involvement in various expected functions such as cytoskeleton organization, nuclear integrity and adhesion, a large number of the predicted substrates are remarkably associated with the development of nerve tissues.Caspases are a family of intracellular cysteinyl aspartate-specific proteases that are highly conserved in multicellular organisms and are key regulators o
In Silico Prediction and In Vivo Validation of Daphnia pulex Micrornas  [PDF]
Shuai Chen, Garrett J. McKinney, Krista M. Nichols, Maria S. Sepúlveda
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0083708
Abstract: Daphnia pulex, the crustacean with the first sequenced genome, is an important organism that has been widely used in ecological and toxicological research. MicroRNAs (miRNAs) are 21–25 nucleotide small non-coding RNAs that are involved in a myriad of physiological processes. In this research, we predicted 75 D. pulex miRNAs by sequence homology and secondary structure identification from the full genome sequence. Fourteen predicted miRNAs were selected for quantitative real time polymerase chain reaction (RT-PCR) validation. Out of these, eight (mir-8, mir-9, mir-12, mir-92, mir-100, mir-133, mir-153 and mir-283) were successfully amplified and validated. Next, expression levels were quantified at three different life stages (days 4, 8 and 12 of age) using U6 spliceosomal RNA as a reference gene. The expression of mir-8, mir-9, mir-12, mir-92 and mir-100 significantly differed across time suggesting these microRNAs might play a critical role during D. pulex development. This is the first study to identify and validate miRNAs in D. pulex, which is an important first step in further studies that evaluate their roles in development and response to environmental and ecological stimuli.
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