Integrating Biological Databases

Lacroix, Zoé; Ludaescher, Bertram; Stevens, Robert

doi:10.1002/9783527619368.ch42

Cited by 4 publications

(2 citation statements)

References 53 publications

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“…Workflow systems are very successful among the biological community as they provide scientists with the ability to express their scientific protocols as a sequence of connected steps [22]. They describe the scientific process from experiment design, data capture, integration, processing, and analysis that leads to scientific discovery.…”

Section: Scientific Workflowsmentioning

confidence: 99%

A Workflow for the Prediction of the Effects of Residue Substitution on Protein Stability

Acuna

Lacroix

Chomilier

2013

Pattern Recognition in Bioinformatics

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The effects of residue substitution in protein can be dramatic and predicting its impact may benefit scientists greatly. Like in many scientific domains there are various methods and tools available to address the potential impact of a mutation on the structure of a protein. The identification of these methods, their availability, the time needed to gain enough familiarity with them and their interface, and the difficulty of integrating their results in a global view where all view points can be visualized often limit their use. In this paper, we present the Structural Prediction for pRotein fOlding UTility System (SPROUTS) workflow and describe our method for designing, documenting, and maintaining the workflow. The focus of the workflow is the thermodynamic contribution to stability, which can be considered as acceptable for small proteins. It compiles the predictions from various sources calculating the ΔΔG upon point mutation, together with a consensus from eight distinct algorithms, with a prediction of the mean number of interacting residues during the process of folding, and a sub domain structural analysis into fragments that may potentially be considered as autonomous folding units, i.e., with similar conformations alone and in the protein body. The workflow is implemented and available online. We illustrate its use with the analysis of the engrailed homeodomain (PDB code 1enh).

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Section: Scientific Workflowsmentioning

confidence: 99%

A Workflow for the Prediction of the Effects of Residue Substitution on Protein Stability

Acuna

Lacroix

Chomilier

2013

Pattern Recognition in Bioinformatics

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“…Classification algorithms involve statistical methods such as Support Vector Mechine (SVM), Decision Trees and Bayesian Network have been most popularly used. Nevertheless with the advent of AI techniques, these have been employed extensively for classification [100][101][102][103][104][105][106].…”

Section: Ai In Genomic Expression Profilingmentioning

confidence: 99%

Artificial Intelligence in Biological Data

Chakraborty¹,

Choudhury²

2017

J Inform Tech Softw Eng

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Artificial Intelligence (AI) or Machine learning in present era, serves as the primary choice for data mining and big data analysis. With effective learning and adaptation model, it provides solutions to several engineering applications. These include techniques such as Artificial Neural Network modelling, Reasoning based decision algorithms, Simulation models, DNA computing and Quantum computing among several others. With the application of AI in Biomedical research, the fuzziness and randomness in handling such type of data has significantly reduced. Rapid technological advancements have helped AI techniques evolve in manner which promotes handling such fuzzy data effectively and much more conveniently. The review presents a comprehensive view of machine learning and AI computing models, advanced data analytics and optimisation approaches used in Bioengineering such as Drug Designing and Analysis, Medical imaging, biologically inspired learning and adaption for analytics, etc.

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Query Languages for the Life Sciences

Lacroix¹

2018

Encyclopedia of Database Systems

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Integrating Biological Databases

Cited by 4 publications

References 53 publications

A Workflow for the Prediction of the Effects of Residue Substitution on Protein Stability

A Workflow for the Prediction of the Effects of Residue Substitution on Protein Stability

Artificial Intelligence in Biological Data

Query Languages for the Life Sciences

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