@article {68,
	title = {Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation.},
	journal = {Structure},
	volume = {24},
	year = {2016},
	month = {2016 05 03},
	pages = {826-837},
	abstract = {<p>The rapidly growing volume of data being produced by next-generation sequencing initiatives is enabling more in-depth analyses of conservation than previously possible. Deep sequencing is uncovering disease loci and regions under selective constraint, despite the fact that intuitive biophysical reasons for such constraint are sometimes absent. Allostery may often provide the missing explanatory link. We use models of protein conformational change to identify allosteric residues by finding essential surface pockets and information-flow bottlenecks, and we develop a software tool that enables users to perform this analysis on their own proteins of interest. Though fundamentally 3D-structural in nature, our analysis is computationally fast, thereby allowing us to run it across the PDB and to evaluate general properties of predicted allosteric residues. We find that these tend to be conserved over diverse evolutionary time scales. Finally, we highlight examples of allosteric residues that help explain poorly understood disease-associated variants.</p>},
	keywords = {Allosteric Site, Animals, Conserved Sequence, Humans, Proteome, Sequence Analysis, Protein, Software},
	issn = {1878-4186},
	doi = {10.1016/j.str.2016.03.008},
	author = {Clarke, Declan and Sethi, Anurag and Li, Shantao and Kumar, Sushant and Chang, Richard W F and Chen, Jieming and Gerstein, Mark}
}
@article {104,
	title = {Reads meet rotamers: structural biology in the age of deep sequencing.},
	journal = {Curr Opin Struct Biol},
	volume = {35},
	year = {2015},
	month = {2015 Dec},
	pages = {125-34},
	abstract = {<p>Structure has traditionally been interrelated with sequence, usually in the framework of comparing sequences across species sharing a common fold. However, the nature of information within the sequence and structure databases is evolving, changing the type of comparisons possible. In particular, we now have a vast amount of personal genome sequences from human populations and a greater fraction of new structures contain interacting proteins within large complexes. Consequently, we have to recast our conception of sequence conservation and its relation to structure-for example, focusing more on selection within the human population. Moreover, within structural biology there is less emphasis on the discovery of novel folds and more on relating structures to networks of protein interactions. We cover this changing mindset here. </p>},
	keywords = {High-Throughput Nucleotide Sequencing, Humans, Isomerism, Mutation, Proteins},
	issn = {1879-033X},
	doi = {10.1016/j.sbi.2015.11.003},
	author = {Sethi, Anurag and Clarke, Declan and Chen, Jieming and Kumar, Sushant and Galeev, Timur R and Regan, Lynne and Gerstein, Mark}
}
