Structured Probabilistic Models of Proteins across Spatial and Fitness Landscapes

Structured Probabilistic Models of Proteins across Spatial and Fitness Landscapes (2011)

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by Hetunandan Kamichetty , Jaime Carbonell

BibTeX

@MISC{Kamichetty11structuredprobabilistic,
    author = {Hetunandan Kamichetty and Jaime Carbonell},
    title = {Structured Probabilistic Models of Proteins across Spatial and Fitness Landscapes},
    year = {2011}
}

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Abstract

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Citations

2135	Convex Optimization - Boyd, Vandenberghe - 2004
1548	F: Conditional Random Fields: Probabilistic models for segmenting and labeling sequence data - Lafferty, McCallum, et al. - 2001
999	Regression shrinkage and selection via the lasso - Tibshirani - 2006
568	Optimizing search engines using clickthrough data - Joachims - 2002
535	SR: Profile hidden Markov models - Eddy - 1998
504	The protein data bank - Berman, Westbrook, et al. - 2000
483	C.H.: Worst-case equilibria - Koutsoupias, Papadimitriou - 1999
448	Information theory and statistical mechanics - Jaynes - 1957
448	Probabilistic inference using Markov chain Monte Carlo methods - Neal - 1993
439	Haussler D: Hidden Markov models in computational biology. Applications to protein modeling - Krogh, Brown, et al. - 1994
298	Fusion, propagation, and structuring in belief networks - Pearl - 1986
279	Constructing free-energy approximations and generalized belief propagation algorithms - Yedidia, Freeman, et al.
268	Graphical models, exponential families, and variational - Wainwright, Jordan - 2008
252	Learning to rank using gradient descent - Burges, Shaked, et al. - 2005
246	Subjectivity and Correlation in Randomized Strategies - AUMANN - 1974
230	Hughey R: Hidden Markov models for detecting remote protein homologies. Bioinformatics - Karplus, Barrett - 1998
224	Large margin rank boundaries for ordinal regression - Herbrich, Graepel, et al. - 2000
220	Approximating probabilistic inference in Bayesian belief networks is NP-hard - Dagum, Luby - 1993
190	The Pfam protein families database Nucleic Acids - Bateman, Coin, et al. - 2004
188	Correlated Equilibrium as an Expression of Bayesian Rationality,”Econometrica 55 - Aumann - 1987
186	Inferring Phylogenies Sinauer Associates - Felsenstein - 2004
183	The genetical evolution of social behaviour - Hamilton - 1964
177	Song O: A novel genetic system to detect protein-protein interactions. Nature - Fields - 1989
159	The complexity of computing a nash equilibrium - Daskalakis, Goldberg, et al. - 2006
152	Updating quasi-Newton matrices with limited storage - Nocedal - 1980
142	Zur Theorie der Gesellschaftsspiele - Neumann - 1928
124	The logic of animal conflict - Smith, Price, et al. - 1973
114	Karplus M: Effective energy functions for protein structure prediction. Curr Op Struct Biol 2000 - Lazaridis
97	D: Design of a novel globular protein fold with atomic-level accuracy - Kuhlman, Dantas, et al.
96	On the cut polytope - Barahona, Mahjoub - 1986
88	Learning to rank: From pairwise approach to listwise - Cao, Qin, et al. - 2007
79	Efficiency of pseudolikelihood estimation for simple Gaussian fields - BESAG - 1977
78	Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structure classes - Ponder, Richards - 1987
71	Efficient structure learning of Markov networks using l1-regularization - Lee, Ganapathi, et al. - 2006
61	High-dimensional graphical model selection using ℓ1-regularized logistic regression - Wainwright, Ravikumar, et al. - 2006
59	An orientationdependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes - Kortemme, Morozov, et al. - 2003
53	Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations - Guerois, Nielsen, et al. - 2002
52	Correlated mutations and residue contacts in proteins - Gobel, Sander, et al. - 1994
51	D: A simple physical model for binding energy hot spots in protein-protein complexes - Kortemme, Baker
51	The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method - Kumar, Bouzida, et al. - 1992
51	Ranganathan R: Evolutionarily conserved pathways of energetic connectivity in protein families - SW - 1999
47	Statistical potentials extracted from protein structures: how accurate are they - Thomas, Dill - 1996
46	Predicting protein structure using hidden Markov models. Proteins suppl - Karplus, Sjolander, et al. - 1997
45	Approximate inference and protein-folding - Yanover, Weiss
44	A theory of cooperative phenomena - Kikuchi - 1951
33	Markov random fields in statistics - Clifford
33	Application of a self-consistent mean field theory to predict protein side chain conformations and estimate their entropy - Koehl, Delarue - 1994
31	Statistical Theory of Superlattices - Bethe - 1935
31	Correlated equilibria in graphical games - Kakade, Kearns, et al.
31	Protein design by binary patterning of polar and nonpolar amino-acids , Science 262 - Kamtekar, Schiffer, et al. - 1993