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Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins
(Public Library of Science, 2007)
The aim of this work is to elucidate how physical principles of protein design are reflected in natural sequences that evolved in response to the thermal conditions of the environment. Using an exactly solvable lattice ...
A Src-Like Inactive Conformation in the Abl Tyrosine Kinase Domain
(Public Library of Science, 2006)
The improper activation of the Abl tyrosine kinase results in chronic myeloid leukemia (CML). The recognition of an inactive conformation of Abl, in which a catalytically important Asp-Phe-Gly (DFG) motif is flipped by ...
Empirical Bayes Analysis of Quantitative Proteomics Experiments
(Public Library of Science, 2009)
Background: Advances in mass spectrometry-based proteomics have enabled the incorporation of proteomic data into systems approaches to biology. However, development of analytical methods has lagged behind. Here we describe ...
Protein and DNA Sequence Determinants of Thermophilic Adaptation
(Public Library of Science, 2007)
There have been considerable attempts in the past to relate phenotypic trait—habitat temperature of organisms—to their genotypes, most importantly compositions of their genomes and proteomes. However, despite accumulation ...
Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae
(Public Library of Science, 2005)
Covalent modification of histone proteins plays a role in virtually every process on eukaryotic DNA, from transcription to DNA repair. Many different residues can be covalently modified, and it has been suggested that these ...