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» Constraint Programming in Structural Bioinformatics
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CORR
2010
Springer
144views Education» more  CORR 2010»
15 years 1 days ago
CLP-based protein fragment assembly
Abstract. The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments ar...
Alessandro Dal Palù, Agostino Dovier, Feder...
PEPM
2011
ACM
14 years 3 months ago
Calculating tree navigation with symmetric relational zipper
Navigating through tree structures is a core operation in tree processing programs. Most notably, XML processing programs intensively use XPath, the path specification language t...
Yuta Ikeda, Susumu Nishimura
BIBE
2007
IEEE
128views Bioinformatics» more  BIBE 2007»
15 years 6 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
125
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VRML
2004
ACM
15 years 6 months ago
PathSim visualizer: an Information-Rich Virtual Environment framework for systems biology
Increasingly, biology researchers and medical practitioners are using computational tools to model and analyze dynamic systems across scales from the macro to the cellular to the ...
Nicholas F. Polys, Doug A. Bowman, Chris North, Re...
SIGSOFT
2009
ACM
15 years 7 months ago
Graph-based mining of multiple object usage patterns
The interplay of multiple objects in object-oriented programming often follows specific protocols, for example certain orders of method calls and/or control structure constraints...
Tung Thanh Nguyen, Hoan Anh Nguyen, Nam H. Pham, J...