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JCB
2006
107views more  JCB 2006»
9 years 1 months ago
Protein Image Alignment via Piecewise Affine Transformations
Abstract We present a new approach for aligning families of 2D gels. Instead of choosing one of the gels as reference and performing pairwise alignment, we construct an ideal gel t...
Florian A. Potra, Xing Liu, Françoise Seill...
BMCBI
2007
59views more  BMCBI 2007»
9 years 1 months ago
Environment specific substitution tables for thermophilic proteins
Background: Thermophilic organisms are able to live at high temperatures ranging from 50 to > 100°C. Their proteins must be sufficiently stable to function under these extreme...
K. Mizuguchi, M. Sele, Maria Vittoria Cubellis
ESWA
2006
161views more  ESWA 2006»
9 years 1 months ago
Automated trend analysis of proteomics data using an intelligent data mining architecture
Proteomics is a field dedicated to the analysis and identification of proteins within an organism. Within proteomics, two-dimensional electrophoresis (2-DE) is currently unrivalle...
James Malone, Kenneth McGarry, Chris Bowerman
BMCBI
2007
131views more  BMCBI 2007»
9 years 1 months ago
An improved method for identifying functionally linked proteins using phylogenetic profiles
Background: Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein c...
Shawn Cokus, Sayaka Mizutani, Matteo Pellegrini
BMCBI
2007
151views more  BMCBI 2007»
9 years 1 months ago
Identification of hot regions in protein-protein interactions by sequential pattern mining
Background: Identification of protein interacting sites is an important task in computational molecular biology. As more and more protein sequences are deposited without available...
Chen-Ming Hsu, Chien-Yu Chen, Baw-Jhiune Liu, Chih...
BMCBI
2007
131views more  BMCBI 2007»
9 years 1 months ago
Prediction of peptides observable by mass spectrometry applied at the experimental set level
Background: When proteins are subjected to proteolytic digestion and analyzed by mass spectrometry using a method such as 2D LC MS/MS, only a portion of the proteotypic peptides a...
William S. Sanders, Susan M. Bridges, Fiona M. McC...
BMCBI
2007
202views more  BMCBI 2007»
9 years 1 months ago
ProtNet: a tool for stochastic simulations of protein interaction networks dynamics
Background: Protein interactions support cell organization and mediate its response to any specific stimulus. Recent technological advances have produced large data-sets that aim ...
Massimo Bernaschi, Filippo Castiglione, Alessandra...
BMCBI
2007
124views more  BMCBI 2007»
9 years 1 months ago
Protein structural similarity search by Ramachandran codes
Background: Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed...
Wei-Cheng Lo, Po-Jung Huang, Chih-Hung Chang, Ping...
BMCBI
2007
106views more  BMCBI 2007»
9 years 1 months ago
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive as
Background: A widely-used approach for discovering functional and physical interactions among proteins involves phylogenetic profile comparisons (PPCs). Here, proteins with simila...
Raja Jothi, Teresa M. Przytycka, L. Aravind
IJBRA
2008
63views more  IJBRA 2008»
9 years 1 months ago
Protein cavity clustering based on community structure of pocket similarity network
: Functions of a protein are mainly determined by its structure. Surface cavities, also called pockets or clefts, are ordinarily regarded as potentially active sites where the prot...
Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zh...
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