Bioinformatic Insights Into Mammalian Gene Regulation: Can Keystrokes Confront Cancer?

submitted by: WomenInBioinformatics

Dr. Laura Elnitski, Head of the Genomic Functional Analysis Section, Genome Technology Branch NHGRI/NIH

Dr. Elnitski uses experimental and Bioinformatic methods to discover non-coding functional elements in the human genome.

On 7 March 2008, Dr. Elnitski came to MSU-Bozeman to participate in the Women In Bioinformatics Seminar Series.

Antibody-protein interactions: benchmark datasets and prediction tools evaluation

linked profile(s): juliap
submitted by: apryl
Background The ability to predict antibody binding sites (aka antigenic determinants or B-cell epitopes) for a given protein is a precursor to new vaccine design and diagnostics. Among the various methods of B-cell epitope identification X-ray crystallography is one of the most reliable methods. Using these experimental data computational methods exist for B-cell epitope prediction. As the number of structures of antibody-protein complexes grows, further interest in prediction...
Authors: Julia v Ponomarenko, Philip e Bourne

Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma

linked profile(s): Rommie, SDSC
submitted by: apryl
RNA editing ligase 1 (TbREL1) is required for the survival of both the insect and bloodstream forms of Trypanosoma brucei, the parasite responsible for the devastating tropical disease African sleeping sickness. The type of RNA editing that TbREL1 is involved in is unique to the trypanosomes, and no close human homolog is known to exist. In addition, the high-resolution crystal structure revealed several unique features of the active site, making this enzyme a promising target for...
Authors: Rommie e. Amaro, Robert v. Swift, J. andrew Mccammon

Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry

submitted by: cdupont
Because of the rise in atmospheric oxygen 2.3 billion years ago (Gya) and the subsequent changes in oceanic redox state over the last 2.3–1 Gya, trace metal bioavailability in marine environments has changed dramatically. Although theorized to have influenced the biological usage of metals leaving discernable genomic signals, a thorough and quantitative test of this hypothesis has been lacking. Using structural bioinformatics and whole-genome sequences, the Fe-, Zn-, Mn-, and...
Authors: Christopher l. Dupont, Song Yang, Brian Palenik, Philip e. Bourne

Wiggle—Predicting Functionally Flexible Regions from Primary Sequence

submitted by: jgu
The Wiggle series are support vector machine–based predictors that identify regions of functional flexibility using only protein sequence information. Functionally flexible regions are defined as regions that can adopt different conformational states and are assumed to be necessary for bioactivity. Many advances have been made in understanding the relationship between protein sequence and structure. This work contributes to those efforts by making strides to understand the relationship...
Authors: Jenny Gu, Michael Gribskov, Philip E Bourne

Structural Evolution of the Protein Kinase–Like Superfamily

linked profile(s): Phil
submitted by: escheeff
The protein kinase family is large and important, but it is only one family in a larger superfamily of homologous kinases that phosphorylate a variety of substrates and play important roles in all three superkingdoms of life. We used a carefully constructed structural alignment of selected kinases as the basis for a study of the structural evolution of the protein kinase–like superfamily. The comparison of structures revealed a “universal core” domain consisting only of...
Authors: Eric d Scheeff, Philip e Bourne