Antibody-protein interactions: benchmark datasets and prediction tools evaluation

wugongliang submitted, created time 1 year 3 months (www.biomedcentral.com)

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 methods using 3D structure is anticipated

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Researchers Determine Structure Of Protein From Pathogen Associated With Cystic Fibrosis And Tuberculosis

Cindy submitted, created time 1 year 5 months (www.sciencedaily.com)

The structure of a novel protein in the bacterium that is the most persistent pathogen in cystic fibrosis (CF) patients has been solved.

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Structural basis for conserved complement factor-like function in the antimalarial protein TEP1

Reviver submitted, created time 1 year 5 months (www.pnas.org)

"Thioester-containing proteins (TEPs) are a major component of the innate immune response of insects to invasion by bacteria and protozoa. TEPs form a distinct clade of a superfamily that includes the pan-protease inhibitors {alpha}2-macroglobulins and vertebrate complement factors. The essential feature of these proteins is a sequestered thioester bond that, after cleavage in a protease-sensitive region of the protein, is activated and covalently binds to its target

Submit comment | Blog It | Email It | Keywords: TEP1 alleles protein structure Thioester-containing proteins

Proportion of Solvent-Exposed Amino Acids in a Protein and Rate of Protein Evolution

fiona submitted, created time 1 year 8 months (mbe.oxfordjournals.org)

"Translational selection, including gene expression, protein abundance, and codon usage bias, has been suggested as the single dominant determinant of protein evolutionary rate in yeast."

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PROTMAP2D: visualization, comparison, and analysis of 2D maps of protein structure

claudia submitted, created time 1 year 8 months (bioinformatics.oxfordjournals.org)

Protein structure comparison is a fundamental problem in structural biology and bioinformatics. Two-dimensional maps of distances between residues in the structure contain sufficient information to restore the 3D representation, while maps of contacts reveal characteristic patterns of interactions between secondary and super-secondary structures and are very attractive for visual analysis. The overlap of 2D maps of two structures can be easily calculated, providing a sensitive measure of protein structure similarity

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T. Rex Related to Chickens

channel submitted, created time 1 year 8 months (www.livescience.com)

An adolescent female Tyrannosaurus rex died 68 million years ago, but its bones still contain intact soft tissue, including the oldest preserved proteins ever found, scientists say. And a comparison of the protein’s chemical structure to a slew of other species showed an evolutionary link between T. rex and chickens, bolstering the idea that birds evolved from dinosaurs.

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Site-specific protein modification: advances and applications

julie submitted, created time 1 year 9 months (www.sciencedirect.com)

"Although chemical methods to modify proteins in a sequence-specific manner have yet to be developed, site-specific post-translational modification of proteins has recently emerged as a major focus in biological chemistry. Post-translational modification with functionalized substrate analogues opens up several unique avenues to induce selective reactivity into proteins in a sequence-specific manner, and can be applied to protein identification and manipulation in both in vitro and in vivo contexts

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