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BMCBI
2011
10 years 6 months ago
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring
Background: Since its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. I...
Mi-Youn K. Brusniak, Sung-Tat Kwok, Mark Christian...
BMCBI
2011
10 years 6 months ago
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning
Background: Accurate identification of protein domain boundaries is useful for protein structure determination and prediction. However, predicting protein domain boundaries from a...
Jesse Eickholt, Xin Deng, Jianlin Cheng
BMCBI
2010
145views more  BMCBI 2010»
10 years 6 months ago
Directionality in protein fold prediction
Background: Ever since the ground-breaking work of Anfinsen et al. in which a denatured protein was found to refold to its native state, it has been frequently stated by the prote...
Jonathan J. Ellis, Fabien P. E. Huard, Charlotte M...
BMCBI
2010
123views more  BMCBI 2010»
10 years 6 months ago
Predicting conserved protein motifs with Sub-HMMs
Background: Profile HMMs (hidden Markov models) provide effective methods for modeling the conserved regions of protein families. A limitation of the resulting domain models is th...
Kevin Horan, Christian R. Shelton, Thomas Girke
BMCBI
2010
131views more  BMCBI 2010»
10 years 6 months ago
Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity
Background: The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In or...
Márton Münz, Rune B. Lyngsø, Jo...
BMCBI
2010
102views more  BMCBI 2010»
10 years 6 months ago
Predicting protein-protein interactions in unbalanced data using the primary structure of proteins
Background: Elucidating protein-protein interactions (PPIs) is essential to constructing protein interaction networks and facilitating our understanding of the general principles ...
Chi-Yuan Yu, Lih-Ching Chou, Darby Tien-Hao Chang
CORR
2009
Springer
106views Education» more  CORR 2009»
10 years 9 months ago
A framework for protein and membrane interactions
dels at different abstraction levels; in particular, higher-level (e.g. membrane) activities can be given a formal biological justification in terms of low-level (i.e., protein) in...
Giorgio Bacci, Davide Grohmann, Marino Miculan
PRIB
2010
Springer
176views Bioinformatics» more  PRIB 2010»
10 years 9 months ago
An On/Off Lattice Approach to Protein Structure Prediction from Contact Maps
Abstract. An important unsolved problem in structural bioinformatics is that of protein structure prediction (PSP), the reconstruction of a biologically plausible three-dimensional...
Stefano Teso, Cristina Di Risio, Andrea Passerini,...
ISBRA
2010
Springer
10 years 9 months ago
Residue Contexts: Non-sequential Protein Structure Alignment Using Structural and Biochemical Features
The study of non-sequential alignments, with different connectivity of the aligned fragments in the proteins being compared can offer a more complete picture of the structural, evo...
Jay W. Kim, Rahul Singh
GCB
2010
Springer
122views Biometrics» more  GCB 2010»
10 years 10 months ago
Quantitative Comparison of Genomic-Wide Protein Domain Distributions
Abstract: Investigations into the origins and evolution of regulatory mechanisms require quantitative estimates of the abundance and co-occurrence of functional protein domains amo...
Arli A. Parikesit, Peter F. Stadler, Sonja J. Proh...
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