- The Oxford Handbook of Applied Bayesian Analysis
- Preface
- List of Contributors
- Flexible Bayes regression of epidemiologic data
- Bayesian modelling for matching and alignment of biomolecules
- Bayesian approaches to aspects of the Vioxx trials: Non-ignorable dropout and sequential meta-analysis
- Sensitivity analysis in microbial risk assessment: Vero-cytotoxigenic <i>E. coli</i> O157 in farm-pasteurized milk
- Mapping malaria in the Amazon rain forest: A spatio-temporal mixture model
- Trans-study projection of genomic biomarkers in analysis of oncogene deregulation and breast cancer
- Linking systems biology models to data: A stochastic kinetic model of p53 oscillations
- Paternity testing allowing for uncertain mutation rates
- Bayesian analysis and decisions in nuclear power plant maintenance
- Bayes linear uncertainty analysis for oil reservoirs based on multiscale computer experiments
- Bayesian modelling of train door reliability
- Analysis of economic data with multiscale spatio-temporal models
- Extracting S&P500 and NASDAQ Volatility: The Credit Crisis of 2007–2008
- Futures markets, Bayesian forecasting and risk modelling
- The new macroeconometrics: A Bayesian approach
- Assessing the probability of rare climate events
- Models for demography of plant populations
- Combining monitoring data and computer model output in assessing environmental exposure
- Indirect elicitation from ecological experts: From methods and software to habitat modelling and rock-wallabies
- Characterizing the uncertainty of climate change projections using hierarchical models
- Volatility in prediction markets: A measure of information flow in political campaigns
- Bayesian analysis in item response theory applied to a large-scale educational assessment
- Sequential multilocation auditing and the New York food stamps program
- Bayesian causal inference: Approaches to estimating the effect of treating hospital type on cancer survival in Sweden using principal stratification
- Bayesian statistical methods for audio and music processing
- Combining simulations and physical observations to estimate cosmological parameters
- Probabilistic grammars and hierarchical Dirichlet processes
- Designing and analysing a circuit device experiment using treed Gaussian processes
- Multistate models for mental fatigue
- Index
Abstract and Keywords
This article describes Bayesian modelling for matching and alignment of biomolecules. One particular task where statistical modelling and inference can be useful in scientific understanding of protein structure is that of matching and alignment of two or more proteins. In this regard, statistical shape analysis potentially has something to offer in solving biomolecule matching and alignment problems. The article discusses the use of Bayesian methods for shape analysis to assist with understanding the three-dimensional structure of protein molecules, with a focus on the problem of matching instances of the same structure in the CoMFA (Comparative Molecular Field Analysis) database of steroid molecules. It introduces a Bayesian hierarchical model for pairwise matching and for alignment of multiple configurations before concluding with an overview of some advantages of the Bayesian approach to problems in protein bioinformatics, along with modelling and computation issues, alternative approaches, and directions for future research.
Keywords: Bayesian modelling, biomolecule matching and alignment, biomolecules, protein structure, shape analysis, Bayesian methods, hierarchical model, pairwise matching, protein bioinformatics
Peter J. Green, School of Mathematics, University of Bristol, Bristol, BS8 1TW, UK
Kanti V. Mardia, Department of Statistics, University of Leeds, Leeds, LS2 9JT, UK
Vysaul B. Nyirongo, MLW Clinical Research Programme, College of Medicine, University of Malawi, Blantyre 3, Malawi
Yann Ruffieux, FSB IMA STAT Station 8, EPFL - Swiss Federal Institute of Technology, CH - 1015 Ecublens, Switzerland
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- The Oxford Handbook of Applied Bayesian Analysis
- Preface
- List of Contributors
- Flexible Bayes regression of epidemiologic data
- Bayesian modelling for matching and alignment of biomolecules
- Bayesian approaches to aspects of the Vioxx trials: Non-ignorable dropout and sequential meta-analysis
- Sensitivity analysis in microbial risk assessment: Vero-cytotoxigenic <i>E. coli</i> O157 in farm-pasteurized milk
- Mapping malaria in the Amazon rain forest: A spatio-temporal mixture model
- Trans-study projection of genomic biomarkers in analysis of oncogene deregulation and breast cancer
- Linking systems biology models to data: A stochastic kinetic model of p53 oscillations
- Paternity testing allowing for uncertain mutation rates
- Bayesian analysis and decisions in nuclear power plant maintenance
- Bayes linear uncertainty analysis for oil reservoirs based on multiscale computer experiments
- Bayesian modelling of train door reliability
- Analysis of economic data with multiscale spatio-temporal models
- Extracting S&P500 and NASDAQ Volatility: The Credit Crisis of 2007–2008
- Futures markets, Bayesian forecasting and risk modelling
- The new macroeconometrics: A Bayesian approach
- Assessing the probability of rare climate events
- Models for demography of plant populations
- Combining monitoring data and computer model output in assessing environmental exposure
- Indirect elicitation from ecological experts: From methods and software to habitat modelling and rock-wallabies
- Characterizing the uncertainty of climate change projections using hierarchical models
- Volatility in prediction markets: A measure of information flow in political campaigns
- Bayesian analysis in item response theory applied to a large-scale educational assessment
- Sequential multilocation auditing and the New York food stamps program
- Bayesian causal inference: Approaches to estimating the effect of treating hospital type on cancer survival in Sweden using principal stratification
- Bayesian statistical methods for audio and music processing
- Combining simulations and physical observations to estimate cosmological parameters
- Probabilistic grammars and hierarchical Dirichlet processes
- Designing and analysing a circuit device experiment using treed Gaussian processes
- Multistate models for mental fatigue
- Index
