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257views Computer Vision» more  NAR 2011»
11 years 8 months ago
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
An essential prerequisite for any systems-level understanding of cellular functions is to correctly uncover and annotate all functional interactions among proteins in the cell. To...
Damian Szklarczyk, Andrea Franceschini, Michael Ku...
12 years 19 days 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
124views more  NAR 2007»
12 years 5 months ago
EVEREST: a collection of evolutionary conserved protein domains
Protein domains are subunits of proteins that recur throughout the protein world. There are many definitions attempting to capture the essence of a protein domain, and several sys...
Elon Portugaly, Nathan Linial, Michal Linial
108views more  BMCBI 2004»
12 years 5 months ago
Enhanced protein domain discovery using taxonomy
Background: It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not ...
Lachlan James M. Coin, Alex Bateman, Richard Durbi...
97views more  BMCBI 2005»
12 years 5 months ago
Comparative mapping of sequence-based and structure-based protein domains
Background: Protein domains have long been an ill-defined concept in biology. They are generally described as autonomous folding units with evolutionary and functional independenc...
Ya Zhang, John-Marc Chandonia, Chris H. Q. Ding, S...
100views more  NAR 2008»
12 years 5 months ago
DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture
We present DAhunter, a web-based server that identifies homologous proteins by comparing domain architectures, the organization of protein domains. A major obstacle in comparison ...
Byungwook Lee, Doheon Lee
12 years 9 months ago
Prediction of Domain-Domain Interactions Using Inductive Logic Programming from Multiple Genome Databases
Protein domains are the building blocks of proteins, and their interactions are crucial in forming stable protein-protein interactions (PPI) and take part in many cellular processe...
Thanh Phuong Nguyen, Tu Bao Ho
142views Bioinformatics» more  BIBE 2007»
12 years 12 months ago
An HV-SVM Classifier to Infer TF-TF Interactions Using Protein Domains and GO Annotations
—Interactions between transcription factors (TFs) are necessary for deciphering the complex mechanisms of transcription regulation in eukaryotes. In this paper, we proposed a nov...
Xiaoli Li, Jun-Xiang Lee, Bharadwaj Veeravalli, Se...
120views Bioinformatics» more  PRIB 2009»
13 years 5 days ago
Knowledge-Guided Docking of WW Domain Proteins and Flexible Ligands
Studies of interactions between protein domains and ligands are important in many aspects such as cellular signaling. We present a knowledge-guided approach for docking protein dom...
Haiyun Lu, Hao Li, Shamima Banu Bte Sm Rashid, Wee...