New Methods from the Berkeley Phylogenomics Group

submitted by: ruchira

Here we present two new algorithms hosted within the PhyloFacts phylogenomic encyclopedias.

Bookcast - Structural Bioinformatics 2nd Edition Gu & Bourne (Eds.)

submitted by: Phil
Further details of the book can be found at and on Google Books .

The Biology of Genomes (2008) with Joseph Ecker Interviewed by Jan Witkowsk

Joseph Ecker is a Professor in the Plant Biology Laboratory and the Director of the Genomic Analysis Laboratory at The Salk Institute for Biological Studies in La Jolla, Ca. He earned his Ph.D. in Microbiology at the Pennsylvania State University College of Medicine and carried out postdoctoral studies with Ronald Davis at the Department of Biochemistry at Stanford University. He served on the Faculty at the University of Pennsylvania (1987-2000) before joining The Salk Institute for...

Bacterial Inclusion Bodies Contain Amyloid-Like Structure

linked profile(s): Lei Wang
submitted by: apryl
Protein aggregation is a process in which identical proteins self-associate into imperfectly ordered macroscopic entities. Such aggregates are generally classified as amorphous, lacking any long-range order, or highly ordered fibrils. Protein fibrils can be composed of native globular molecules, such as the hemoglobin molecules in sickle-cell fibrils, or can be reorganized β-sheet–rich aggregates, termed amyloid-like fibrils. Amyloid fibrils are associated with several...
Authors: David Eisenberg, Samir K Maji, Roland Riek, Michael R Sawaya, Lei Wang

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

Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus

submitted by: art
CD8+ cytotoxic T-lymphocytes (CTLs) perform a critical role in the immune control of viral infections, including those caused by human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV). As a result, genetic variation at CTL epitopes is strongly influenced by host-specific selection for either escape from the immune response, or reversion due to the replicative costs of escape mutations in the absence of CTL recognition. Under strong CTL-mediated selection, codon positions...
Authors: Art f. y Poon, Sergei l. kosakovsky Pond, Phil Bennett, Douglas d Richman, Andrew j. leigh Brown, Simon d. w Frost

Multipolar representation of protein structure

linked profile(s): Phil
submitted by: jmath
Background That the structure determines the function of proteins is a central paradigm in biology. However, protein functions are more directly related to cooperative effects at the residue and multi-residue scales. As such, current representations based on atomic coordinates can be considered inadequate. Bridging the gap between atomic-level structure and overall protein-level functionality requires parameterizations of the protein structure (and other...
Authors: Apostol Gramada, 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