Michael Schatz at the 2012 DOE JGI Genomics of Energy & Environment Meeting

submitted by: JGI

Michael Schatz from Cold Spring Harbor Laboratory on "Entering the Era of Mega-genomics" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

David Jaffe and Sante Gnerre on "Visualizing assembling everything"

submitted by: JGI

David Jaffe and Sante Gnerre of the Broad Institute present at the JGI/Argonne HPC Workshop on January 25, 2010.

Large-scale Phosphorylation Analysis (Proteomics): Dr. Sean Beausoleil, Harvard

submitted by: dachian

Analyzing phosphopeptides using proteomics mass spectrometry is challenging, especially for large-scale data sets. The problem and solution is discussed by Dr. Sean Beausoleil (Harvard Medical School), who is the co-inventor of the ASCORE algorithm for phosphorylation site localization.

Molecular Representation, Similarity and Search

submitted by: jcbradley
Rajarshi Guha presents at the final fall 09 Chemical Information Retrieval class at Drexel University on December 3, 2009. The audio for the first 45 seconds is a little off but the rest is fine. Implicit and explicit molecular representations in 1D, 2D and 3D formats are introduced. Approaches to quantifying molecular similarity using fingerprinting are discussed, such as the Tanimoto index. The relevance of these methods to drug design in terms of virtual screening and QSAR is explored....

Evolution of Reproductive Morphology in Leaf Endophytes

submitted by: JeffreyTownsend
The endophytic lifestyle has played an important role in the evolution of the morphology of reproductive structures (body) in one of the most problematic groups in fungal classification, the Leotiomycetes (Ascomycota). Mapping fungal morphologies to two groups in the Leiotiomycetes, the Rhytismatales and Hemiphacidiaceae reveals significant divergence in body size, shape and complexity. Mapping ecological roles to these taxa reveals that the groups include endophytic fungi living on leaves...
Authors: Zheng Wang, Peter R. Johnston, Zhu L. Yang, Jeffrey P. Townsend

Translational Proteomics 2.0 Meeting: SEQUEST and TPP Tips

submitted by: dachian

Advanced tips on using SEQUEST and TPP by Jimmy Eng of U. of Washington, the co-inventor of SEQUEST

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