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Solving the protein folding problem

A Listmania! list by A reader (Copenhagen, Denmark)
 
Protein Physics: A Course of Lectures (Soft Condensed Matter, Complex Fluids and Biomaterials)
1.  Protein Physics: A Course of Lectures (Soft Condensed Matter, Complex Fluids and Biomaterials) by Alexei V. Finkelstein
The list author says:
  "Very accessible, insightful book by two pioneers of the field. Very good illustrations too."
65.79   Used & New from: 55.82
5.0 out of 5 stars  See all reviews (3 customer reviews)

Directional Statistics
2.  Directional Statistics by Kanti V. Mardia
The list author says:
  "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!"
116.09   Used & New from: 88.44
5.0 out of 5 stars  See all reviews (1 customer review)

Introduction to Protein Structure
3.  Introduction to Protein Structure by Carl Ivar Branden
The list author says:
  "A great pictorial overview of protein geometry and structure."
49.88   Used & New from: 24.80
4.8 out of 5 stars  See all reviews (4 customer reviews)

Structure and Mechanism in Protein Science: Guide to Enzyme Catalysis and Protein Folding
4.  Structure and Mechanism in Protein Science: Guide to Enzyme Catalysis and Protein Folding by Alan Fersht
The list author says:
  "Classic reference on proteins (enzyme mechanism, protein stability, kinetics of folding,...). Concise, lots of references."
Used & New from: 70.00
4.0 out of 5 stars  See all reviews (2 customer reviews)

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Molecular Driving Forces: Statistical Thermodynamics in Chemistry, Physics, Biology, and Nanoscience: Statistical Thermodynamics in Chemistry and Biology
5.  Molecular Driving Forces: Statistical Thermodynamics in Chemistry, Physics, Biology, and Nanoscience: Statistical Thermodynamics in Chemistry and Biology by Sarina Bromberg
The list author says:
  "Nice introduction to thermodynamics & statistical mechanics. Lots of relevant protein-related topics (like the Zimm-Bragg model of helix-coil transition)."
45.00   Used & New from: 29.99

Computational Geometry: Algorithms and Applications
6.  Computational Geometry: Algorithms and Applications by Mark de Berg
The list author says:
  "From KD-trees to Voronoi diagrams. A pleasure to read. Plenty of clear pseudo code."
Used & New from: 12.03
4.3 out of 5 stars  See all reviews (3 customer reviews)

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Learning in Graphical Models (Adaptive Computation and Machine Learning) (Adaptive Computation and Machine Learning Series)
7.  Learning in Graphical Models (Adaptive Computation and Machine Learning) (Adaptive Computation and Machine Learning Series) by Michael Jordan
The list author says:
  "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."
45.23   Used & New from: 32.64
4.0 out of 5 stars  See all reviews (1 customer review)

Learning Bayesian Networks (Artificial Intelligence)
8.  Learning Bayesian Networks (Artificial Intelligence) by Richard E. Neapolitan
The list author says:
  "Thorough covering of Bayesian Networks. Emphasis on deterministic, exact algorithms. Start with this, and then proceed to Jordan's book."
95.35   Used & New from: 70.75

Markov Chain Monte Carlo in Practice (Chapman & Hall/CRC Interdisciplinary Statistics Series)
9.  Markov Chain Monte Carlo in Practice (Chapman & Hall/CRC Interdisciplinary Statistics Series) by W.R. Gilks
The list author says:
  "A classic on probabilistic applications of MCMC methods."
80.10   Used & New from: 37.76
5.0 out of 5 stars  See all reviews (2 customer reviews)

Probability Theory: The Logic of Science: Principles and Elementary Applications Vol 1
10.  Probability Theory: The Logic of Science: Principles and Elementary Applications Vol 1 by E. T. Jaynes
The list author says:
  "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."
53.55   Used & New from: 47.76
4.6 out of 5 stars  See all reviews (8 customer reviews)

Matrix Computations (Johns Hopkins Studies in the Mathematical Sciences)
11.  Matrix Computations (Johns Hopkins Studies in the Mathematical Sciences) by Gene H. Golub
The list author says:
  "For all those matrix problems (starting with optimal RMSD calculation of course!)"
25.73   Used & New from: 19.00
5.0 out of 5 stars  See all reviews (5 customer reviews)

Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
12.  Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids by Richard Durbin
The list author says:
  "The first book you need on Bioinformatics. Emphasis on probabilistic models and associated algorithms. Very clearly written."
28.04   Used & New from: 21.13
3.7 out of 5 stars  See all reviews (3 customer reviews)

Bioinformatics: The Machine Learning Approach (Adaptive Computation and Machine Learning Series)
13.  Bioinformatics: The Machine Learning Approach (Adaptive Computation and Machine Learning Series) by Pierre Baldi
The list author says:
  "The second book you need on Bioinformatics. More theoretical. Also based on probabilistic models. Covers a lot of ground, but can be quite cryptic."
42.83   Used & New from: 11.99
4.5 out of 5 stars  See all reviews (4 customer reviews)

Proteins: Structures and Molecular Properties
14.  Proteins: Structures and Molecular Properties by Thomas E. Creighton
The list author says:
  "Could do with an update, but still a great, accessible reference for protein structure and properties."
65.99   Used & New from: 8.48

Bayesian Statistics: An Introduction (Arnold Publication)
15.  Bayesian Statistics: An Introduction (Arnold Publication) by Peter M Lee
The list author says:
  "Simple, concise introduction to Bayesian statistics."
Used & New from: 27.58

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Pattern Recognition and Machine Learning (Information Science and Statistics)
16.  Pattern Recognition and Machine Learning (Information Science and Statistics) by Christopher M. Bishop
The list author says:
  "Fantastic, thorough overview of machine learning from a Bayesian viewpoint. Beautifully illustrated and an example of clarity, yet rigorous. A gem."
63.99   Used & New from: 36.00
4.2 out of 5 stars  See all reviews (10 customer reviews)

Introduction to Modern Statistical Mechanics
17.  Introduction to Modern Statistical Mechanics by David Chandler
The list author says:
  "Modern treatment of statistical mechanics, including Monte Carlo simulations, Ising models and renormalization group theory.  A bit terse, but very clear and well organized."
Used & New from: 27.17
4.0 out of 5 stars  See all reviews (2 customer reviews)

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Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference (Morgan Kaufmann Series in Representation and Reasoning)
18.  Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference (Morgan Kaufmann Series in Representation and Reasoning) by Judea Pearl
The list author says:
  "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."
43.99   Used & New from: 28.60
4.0 out of 5 stars  See all reviews (1 customer review)

Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach
19.  Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach by Kenneth P. Burnham
The list author says:
  "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."
78.62   Used & New from: 48.99
5.0 out of 5 stars  See all reviews (2 customer reviews)

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A reader (Copenhagen, Denmark)
Qualifications: Structural bioinformatics researcher
Last updated: 08/10/2008
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