Student Book World - Solving the protein folding problem

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Solving the protein folding problem

	Protein Physics: A Course of Lectures (Soft Condensed Matter, Complex Fluids and Biomaterials) by Alexei V. Finkelstein Buy used from: £80.29 Very accessible, insightful book by two pioneers of the field. Very good illustrations too.
	Directional Statistics by Kanti V. Mardia Buy new: £85.50 / Used from: £68.65 Standard work on the statistics of angles, axes and orientations. Not easy, but a treasure trove of probabilistic solutions to common problems in structure prediction, waiting to be uncovered!
	Introduction to Protein Structure by Carl Ivar Branden Buy new: £35.25 / Used from: £30.00 A great pictorial overview of protein geometry and structure.
	Structure and Mechanism in Protein Science: Guide to Enzyme Catalysis and Protein Folding by Alan Fersht Buy new: £45.77 / Used from: £23.50 Classic reference on proteins (enzyme mechanism, protein stability, kinetics of folding,...). Concise, lots of references.
	Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology by Sarina Bromberg Buy new: £38.00 / Used from: £36.50 Nice introduction to thermodynamics & statistical mechanics. Lots of relevant protein-related topics (like the Zimm-Bragg model of helix-coil transition).
	Computational Geometry: Algorithms and Applications by Mark de Berg Buy new: £24.23 / Used from: £44.92 From KD-trees to Voronoi diagrams. A pleasure to read. Plenty of clear pseudo code.
	Learning in Graphical Models (Adaptive Computation and Machine Learning) by MI Jordan Buy new: £45.86 / Used from: £45.79 Probabilistic models are getting more and more important in macromolecular 3D structure prediction. Great reference, and some good tutorial chapters too. Also deals with approximative algorithms.
	Learning Bayesian Networks (Artificial Intelligence) by Richard E. Neapolitan Buy new: £45.99 / Used from: £40.17 Thorough covering of Bayesian Networks. Emphasis on deterministic, exact algorithms. Start with this, and then proceed to Jordan's book.
	Markov Chain Monte Carlo in Practice (Chapman & Hall/CRC Interdisciplinary Statistics Series) by W.R. Gilks Buy new: £57.57 / Used from: £58.07 A classic on probabilistic applications of MCMC methods.
	Probability Theory: The Logic of Science: Principles and Elementary Applications Vol 1 by E. T. Jaynes Buy new: £42.59 / Used from: £58.27 A Bayesian, probabilistic view on science. Provides many relevant general insights. Jaynes pointed out the importance of Bayesian methods for protein structure prediction long ago.
	Matrix Computations (Johns Hopkins Series in the Mathematical Sciences) by Gene H. Golub Buy new: £23.43 / Used from: £19.00 For all those matrix problems (starting with optimal RMSD calculation of course!)
	Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids by Richard Durbin Buy new: £24.63 / Used from: £23.40 The first book you need on Bioinformatics. Emphasis on probabilistic models and associated algorithms. Very clearly written.
	Bioinformatics: The Machine Learning Approach (Adaptive Computation and Machine Learning) by P Baldi Buy new: £46.50 / Used from: £24.28 The second book you need on Bioinformatics. More theoretical. Also based on probabilistic models. Covers a lot of ground, but can be quite cryptic.
	Proteins: Structures and Molecular Properties by Thomas E. Creighton Buy new: £49.89 / Used from: £40.00 Could do with an update, but still a great, accessible reference for protein structure and properties.
	Bayesian Statistics: An Introduction (Arnold Publication) by Peter M Lee Buy used from: £19.99 Simple, concise introduction to Bayesian statistics.
	Pattern Recognition and Machine Learning (Information Science and Statistics) (Information Science and Statistics) by Christopher M. Bishop Buy new: £48.01 / Used from: £40.19 Fantastic, thorough overview of machine learning from a Bayesian viewpoint. Beautifully illustrated and an example of clarity, yet rigorous. A gem.
	Introduction to Modern Statistical Mechanics by David Chandler Buy new: £24.80 / Used from: £16.95 Modern treatment of statistical mechanics, including Monte Carlo simulations, Ising models and renormalization group theory. A bit terse, but very clear and well organized.
	Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference by Judea Pearl Buy new: £62.70 / Used from: £75.14 Read this for deeper insights into the history and development of Bayesian networks. BTW: you'll find the justification of the ROSETTA pairwise energy function in paragraph 3.2.4 on page 110.
	Model Selection and Multi-model Inference: A Practical Information-theoretic Approach by Kenneth P. Burnham Buy new: £52.43 / Used from: £58.14 Picking the best probabilistic model out of a set of possible models is a key problem. Methods based on the Akaike Information Criterion are both conceptually elegant and computationally tractable.