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Category: Thesis

Thesis reference table

Topic specific reference tables: substitution matrices, protein evolution, disordered proteins, protein structure, protein function

Thesis references, sorted by year.

	Has author	Published in	Date published	Paper topic
A Model of Evolutionary Change in Proteins	M. Dayhoff	Atlas of Protein Sequence and Structure	24402231969	Substitution matrices
Amino acid substitution matrices from an information theoretic perspective	Stephen F. Altschul	Journal of Molecular Biology	24484135 June 1991	Substitution matrices
The rapid generation of mutation data matrices from protein sequences	D. T. Jones W. R. Taylor J. M. Thornton	Computer Applications In The Biosciences	24487751 June 1992	Substitution matrices
Intrinsically Unstructured Proteins: Re-assessing the Protein Structure-Function Paradigm	P. E. Wright H. J. Dyson	Journal of Molecular Biology	245147422 October 1999	Disordered proteins Protein function
Predicting Binding Regions within Disordered Proteins	E. C. Garner P. Romero A. K. Dunker C. J. Brown Z. Obradovic	Genome Informatics Workshop	245152714 December 1999	Disordered proteins
Intrinsic Protein Disorder in Complete Genomes	A. K. Dunker P. Romero Z. Obradovic E. C. Garner C. J. Brown	Genome Informatics Workshop	245189718 December 2000	Disordered proteins
Sequence Complexity of Disordered Protein	P. Romero Z. Obradovic X. Li E. C. Garner C. J. Brown A. K. Dunker	Proteins: Structure, Function, and Genetics	24519111 January 2001	Disordered proteins
The protein non-folding problem: amino acid determinants of intrinsic order and disorder	R. M. Williams Z. Obradovic V. Mathura W. Braun J. Young E. C. Garner S. Takayama A. K. Dunker	Pacific Symposium on Biocomputing	245192313 January 2001	Disordered proteins
Intrinsically disordered protein (JMolGraphMod)	A. K. Dunker J. D. Lawson C. J. Brown R. M. Williams P. Romero J. S. Oh C. J. Oldfield A. M. Campen C. M. Ratliff K. W. Hipps J. Ausio M. S. Nissen R. Reeves C. Kang C. R. Kissinger R. W. Bailey M. D. Griswold W. Chiu E. C. Garner Z. Obradovic	Journal of Molecular Graphics and Modelling	24519421 February 2001	Disordered proteins
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach	S. Whelan N. Goldman	Molecular Biology and Evolution	24520311 May 2001	Protein evolution
Evolutionary Rate Heterogeneity in Proteins with Long Disordered Regions	C. J. Brown S. Takayama A. M. Campen P. Vise T. W. Marshall C. J. Oldfield C. J. Williams A. K. Dunker P. E. Wright H. J. Dyson	Journal of Molecular Evolution	24524271 June 2002	Disordered proteins Protein evolution
Intrinsically unstructured proteins	P. Tompa	Trends in Biochemical Sciences	24525491 October 2002	Disordered proteins Protein function
Intrinsically unstructured proteins evolve by repeat expansion	P. Tompa	BioEssays	24528841 September 2003	Disordered proteins Protein evolution
Flavors of Protein Disorder	S. Vucetic C. J. Brown A. K. Dunker Z. Obradovic	Proteins: Structure, Function, and Genetics	24528841 September 2003	Disordered proteins
Protein Evolution with Dependence Among Codons Due to Tertiary Structure	D. M. Robinson D. T. Jones H. Kishino N. Goldman J. L. Thorne	Molecular Biology and Evolution	24529141 October 2003	Protein evolution Protein structure
Different Versions of the Dayhoff Rate Matrix	C. Kosiol N. Goldman	Molecular Biology and Evolution	24534031 February 2005	Substitution matrices
Protein database searches using compositionally adjusted substitution matrices	Stephen F. Altschul John C. Wootton E. Michael Gertz Richa Agarwala Aleksandr Morgulis Alejandro A. Schäffer Yi-Kuo Yu	The FEBS Journal	245365915 October 2005	Substitution matrices
Proportion of Solvent-Exposed Amino Acids in a Protein and Rate of Protein Evolution	Y. S. Lin W. L. Hsu J. K. Hwang W. H. Li	Molecular Biology and Evolution	245413029 January 2007	Protein evolution Disordered proteins
Intrinsic disorder and functional proteomics	P. Radivojac L. M. Iakoucheva C. J. Oldfield Z. Obradovic V. N. Uversky A. K. Dunker	Biophysical Journal	24541611 March 2007	Disordered proteins Protein function

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