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Journals and Conferences
The problem of finding frequent patterns from graph-based datasets is an important one that finds applications in drug discovery, protein structure analysis, XML querying, and social network analysis among others. In this paper we propose a framework to mine frequent large-scale structures, formally defined as frequent <i>topological structures</i>, from… (More)
One of the largest areas of bioinformatic and data mining research has been in the protein domain. These efforts have included protein structure prediction, folding pathway prediction, sequence alignment, ab initio simulation, structure alignment, substructure detection and many others. Substructure detection is generally defined as the mining of a… (More)
Femtosecond transient absorption spectroscopy was used to study singlet diphenylcarbene generated by photodissociation of diphenyldiazomethane with a UV pulse at 266 nm. Absorption by singlet diphenylcarbene was detected and characterized for the first time. Similar band shapes were observed in acetonitrile and in cyclohexane with lambda(max) approximately… (More)
The reactive intermediate produced upon photolysis of 8-azidoadenosine was studied by chemical trapping studies, laser flash photolysis with UV-vis and IR detection, and modern computational chemistry. It is concluded that photolysis of 8-azidoadenosine in aqueous solution releases the corresponding singlet nitrene which rapidly tautomerizes to form a… (More)
Our work is an extension of the MotifMiner algorithm, which was designed to find frequent structural motifs in macromolecules. It is an extensible toolkit and allows for the detection of motifs at varying resolutions, ranging from the atomic scale to the secondary structure level. The interactions between objects (atoms, residues, secondary structures,… (More)
Motivation: Here we present two approaches to solving the substructure similarity problem. The first approach is a parallel version of a previously developed substructure mining algorithm. The second is an algorithm that operates on the protein domain and uses a protein’s amino acid sequence in addition to substructures to determine similarity.
The dynamics of singlet 3,5-dichloro-2-biphenylnitrene and the products of its rearrangement were monitored by pico- and nanosecond laser flash photolysis and the results were consistent with the predictions of DFT and ab initio molecular orbital calculations.