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» A Flexible Algorithm for Pairwise Protein Structure Alignmen...
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138
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BMCBI
2005
119views more  BMCBI 2005»
15 years 3 months ago
The distance-profile representation and its application to detection of distantly related protein families
Background: Detecting homology between remotely related protein families is an important problem in computational biology since the biological properties of uncharacterized protei...
Chin-Jen Ku, Golan Yona
105
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JCB
2000
71views more  JCB 2000»
15 years 3 months ago
Structure Comparison and Structure Patterns
This article investigates aspects of pairwise and multiple structure comparison, and the problem of automatically discover common patterns in a set of structures. Descriptions and...
Ingvar Eidhammer, Inge Jonassen, William R. Taylor
150
Voted
BMCBI
2004
208views more  BMCBI 2004»
15 years 3 months ago
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures
Background: Hidden Markov Models (HMMs) have proven very useful in computational biology for such applications as sequence pattern matching, gene-finding, and structure prediction...
Vadim Alexandrov, Mark Gerstein
167
Voted
BMCBI
2011
14 years 10 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
BIBE
2007
IEEE
128views Bioinformatics» more  BIBE 2007»
15 years 10 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