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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)
BACKGROUND By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. RESULTS Here we describe(More)
Assignment of nuclear Overhauser effect (NOE) data is a key bottleneck in structure determination by NMR. NOE assignment resolves the ambiguity as to which pair of protons generated the observed NOE peaks, and thus should be restrained in structure determination. In the case of intersubunit NOEs in symmetric homo-oligomers, the ambiguity includes both the(More)
Protein structure provides insight into the evolutionary origins, functions, and mechanisms of proteins. We are pursuing a minimalist approach to protein fold identification that characterizes possible folds in terms of consistency of their geometric features with restraints derived from relatively cheap, high-throughput experiments. One such experiment is(More)
Kinases are involved in a variety of diseases such as cancer, diabetes, and arthritis. In recent years, many kinase small molecule inhibitors have been developed as potential disease treatments. Despite the recent advances, selectivity remains one of the most challenging aspects in kinase inhibitor design. To interrogate kinase selectivity, a panel of 45(More)
In these Supplementary Materials, we give the mathematical derivation for the bounding regions of Gq, which are used in the subsection entitled Bounding which is inside the Methods section of the main paper. We have organized these Supplementary Materials as follows. The geometric structure of Gq is described in Section S2. From this geometric structure, we(More)
Symmetric homo-oligomers represent a majority of proteins, and determining their structures helps elucidate important biological processes, including ion transport, signal transduction, and transcriptional regulation. In order to account for the noise and sparsity in the distance restraints used in Nuclear Magnetic Resonance (NMR) structure determination of(More)
Symmetric homo-oligomers are protein complexes with similar subunits arranged symmetrically [10]. Figure 1 illustrates the structure of a symmetric homo-oligomer called phospholamban. Phospholamban is a membrane protein that helps regulate the calcium level inside the cell and hence aids in muscle contraction and relaxation [7]; ion conductance studies [5](More)
We propose building an integrated agent-based simulation environment to find the effective security profile within the budget considerations. The key ideas involved are: dynamic firm profile; behavior based dynamic attacker profile generator; leaming-based IDS, and an evolutionary search via genetic algorithms for the effective security profile. The(More)
The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Abstract Background: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type(More)
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