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» Predicting the beta-helix fold from protein sequence data
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BMCBI
2010
152views more  BMCBI 2010»
13 years 7 months ago
A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry
Background: High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflo...
Chongle Pan, Byung-Hoon Park, William H. McDonald,...
RECOMB
2007
Springer
14 years 7 months ago
Minimizing and Learning Energy Functions for Side-Chain Prediction
Abstract. Side-chain prediction is an important subproblem of the general protein folding problem. Despite much progress in side-chain prediction, performance is far from satisfact...
Chen Yanover, Ora Schueler-Furman, Yair Weiss
RECOMB
2005
Springer
14 years 7 months ago
Predicting Transcription Factor Binding Sites Using Structural Knowledge
Abstract. Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structu...
Tommy Kaplan, Nir Friedman, Hanah Margalit
BMCBI
2006
133views more  BMCBI 2006»
13 years 7 months ago
Choosing negative examples for the prediction of protein-protein interactions
The protein-protein interaction networks of even well-studied model organisms are sketchy at best, highlighting the continued need for computational methods to help direct experim...
Asa Ben-Hur, William Stafford Noble
BIBE
2007
IEEE
128views Bioinformatics» more  BIBE 2007»
14 years 1 months ago
QOMA2: Optimizing the alignment of many sequences
Abstract—We consider the problem of aligning multiple protein sequences with the goal of maximizing the SP (Sum-of-Pairs) score, when the number of sequences is large. The QOMA (...
Xu Zhang, Tamer Kahveci