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» Efficient protein alignment algorithm for protein search
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BMCBI
2008
103views more  BMCBI 2008»
14 years 11 months ago
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model
Background: Protein structure analysis and comparison are major challenges in structural bioinformatics. Despite the existence of many tools and algorithms, very few of them have ...
Mallika Veeramalai, Yuzhen Ye, Adam Godzik
IJCBDD
2008
141views more  IJCBDD 2008»
14 years 11 months ago
CLUSS2: an alignment-independent algorithm for clustering protein families with multiple biological functions
: CLUSS is an algorithm proposed for clustering both alignable and non-alignable protein sequences. However, CLUSS tends to be ineffective on protein datasets that include a large ...
Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski
DATESO
2007
157views Database» more  DATESO 2007»
15 years 1 months ago
Index-Based Approach to Similarity Search in Protein and Nucleotide Databases
When searching databases of nucleotide or protein sequences, finding a local alignment of two sequences is one of the main tasks. Since the sizes of available databases grow const...
David Hoksza, Tomás Skopal
104
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BMCBI
2007
142views more  BMCBI 2007»
14 years 11 months ago
SABERTOOTH: protein structural alignment based on a vectorial structure representation
Background: The task of computing highly accurate structural alignments of proteins in very short computation time is still challenging. This is partly due to the complexity of pr...
Florian Teichert, Ugo Bastolla, Markus Porto
BMCBI
2010
163views more  BMCBI 2010»
14 years 11 months ago
Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity
Background: Computational comparison of two protein structures is the starting point of many methods that build on existing knowledge, such as structure modeling (including modeli...
Zong Hong Zhang, Hwee Kuan Lee, Ivana Mihalek