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ICPPW
2009
IEEE
11 years 3 months ago
A Scalable Parallel Approach for Peptide Identification from Large-Scale Mass Spectrometry Data
Identifying peptides, which are short polymeric chains of amino acid residues in a protein sequence, is of fundamental importance in systems biology research. The most popular appr...
Gaurav Ramesh Kulkarni, Ananth Kalyanaraman, Willi...
BMCBI
2005
122views more  BMCBI 2005»
11 years 5 months ago
A neural strategy for the inference of SH3 domain-peptide interaction specificity
Background: The SH3 domain family is one of the most representative and widely studied cases of so-called Peptide Recognition Modules (PRM). The polyproline II motif PxxP that gen...
Enrico Ferraro, Allegra Via, Gabriele Ausiello, Ma...
BMCBI
2005
85views more  BMCBI 2005»
11 years 5 months ago
Prediction of twin-arginine signal peptides
Background: Proteins carrying twin-arginine (Tat) signal peptides are exported into the periplasmic compartment or extracellular environment independently of the classical Secdepe...
Jannick Dyrløv Bendtsen, Henrik Nielsen, Da...
BMCBI
2007
157views more  BMCBI 2007»
11 years 5 months ago
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational
Background: High-throughput peptide and protein identification technologies have benefited tremendously from strategies based on tandem mass spectrometry (MS/MS) in combination wi...
Nico Pfeifer, Andreas Leinenbach, Christian G. Hub...
BMCBI
2006
146views more  BMCBI 2006»
11 years 5 months ago
A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls
Background: Statistical comparison of peptide profiles in biomarker discovery requires fast, userfriendly software for high throughput data analysis. Important features are flexib...
Mark K. Titulaer, Ivar Siccama, Lennard J. Dekker,...
BMCBI
2006
172views more  BMCBI 2006»
11 years 5 months ago
A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data
Background: Tandem mass spectrometry (MS/MS) is a powerful tool for protein identification. Although great efforts have been made in scoring the correlation between tandem mass sp...
Zhuo Zhang, Shiwei Sun, Xiaopeng Zhu, Suhua Chang,...
BMCBI
2008
93views more  BMCBI 2008»
11 years 5 months ago
A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate
Background: A JavaTM application is presented, which compares large numbers (n > 100) of raw FTICR mass spectra from patients and controls. Two peptide profile matrices can be ...
Mark K. Titulaer, Dana A. N. Mustafa, Ivar Siccama...
BMCBI
2010
86views more  BMCBI 2010»
11 years 5 months ago
The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand
Background: We study the usage of specific peptide platforms in protein composition. Using the pentapeptide as a unit of length, we find that in the universal proteome many pentap...
Giovanni Capone, Giuseppe Novello, Candida Fasano,...
BMCBI
2007
113views more  BMCBI 2007»
11 years 5 months ago
In silico panning for a non-competitive peptide inhibitor
Background: Peptide ligands have tremendous therapeutic potential as efficacious drugs. Currently, more than 40 peptides are available in the market for a drug. However, since cos...
Yukiko Yagi, Kotaro Terada, Takahisa Noma, Kazunor...
BMCBI
2008
173views more  BMCBI 2008»
11 years 5 months ago
Improved machine learning method for analysis of gas phase chemistry of peptides
Background: Accurate peptide identification is important to high-throughput proteomics analyses that use mass spectrometry. Search programs compare fragmentation spectra (MS/MS) o...
Allison Gehrke, Shaojun Sun, Lukasz A. Kurgan, Nat...
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