Chris Bailey-Kellogg

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Identifying residue coupling relationships within a protein family can provide important insights into the family's evolutionary record, and has significant applications in analyzing and optimizing sequence-structure-function relationships. We present the first algorithm to infer an undirected graphical model representing residue coupling in protein(More)
Active data mining is becoming prevalent in applications requiring focused sampling of data relevant to a high-level mining objective. It is especially pertinent in scientific and engineering applications where we seek to characterize a configuration space or design space in terms of spatial aggregates, and where data collection can become costly. Examples(More)
Structural studies of symmetric homo-oligomers provide mechanistic insights into their roles in essential biological processes, including cell signaling and cellular regulation. This paper presents a novel algorithm for homo-oligomeric structure determination, given the subunit structure, that is both complete, in that it evaluates all possible(More)
MOTIVATION Complementing its traditional role in structural studies of proteins, nuclear magnetic resonance (NMR) spectroscopy is playing an increasingly important role in functional studies. NMR dynamics experiments characterize motions involved in target recognition, ligand binding, etc., while NMR chemical shift perturbation experiments identify and(More)
High-throughput, data-directed computational protocols for <i>Structural Genomics</i> (or <i>Proteomics</i>) are required in order to evaluate the protein products of genes for structure and function at rates comparable to current gene-sequencing technology. This paper presents the JIGSAW algorithm, a novel high-throughput, automated approach to protein(More)
Reasoning about spatial data is a key task in many applications , including geographic information systems, meteorological and fluid flow analysis, computer-aided design, and protein structure databases. Such applications often require the identification and manipulation of qualitative spatial representations , for example, to detect whether one " object "(More)
Spatial aggregation is a framework for organizing computations around image-like, analogue representations of physical processes in data interpretation and control tasks. It conceptualizes common computational structures in a class of implemented problem solvers for difficult scientific and engineering problems. It comprises a mechanism, a language, and a(More)
Nuclear magnetic resonance (NMR) spectroscopy allows scientists to study protein structure, dynamics, and interactions in solution. A necessary first step for such applications is determining the resonance assignment, mapping spectral data to atoms and residues in the primary sequence. Automated resonance assignment algorithms rely on information regarding(More)
Protein-protein interactions are governed by the change in free energy upon binding, ΔG = ΔH - TΔS. These interactions are often marginally stable, so one must examine the balance between the change in enthalpy, ΔH, and the change in entropy, ΔS, when investigating known complexes, characterizing the effects of mutations, or designing optimized variants. To(More)
This paper develops an approach for designing protein variants by sampling sequences that satisfy residue constraints encoded in an undirected probabilistic graphical model. Due to evolutionary pressures on proteins to maintain structure and function, the sequence record of a protein family contains valuable information regarding position-specific residue(More)