APDB: a web server to evaluate the accuracy of sequence alignments using structural information
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We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded ...
Sequence motifs are of greater biological importance in nucleotide and protein sequences. The conserved occurrence of identical motifs represents the functional significance and helps to classify the biological sequences. In this paper, a new algorithm is ...
Background The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological know ...
A palladium-catalyzed domino aminopalladation/C-H functionalization sequence has been developed, and provides access to functionalized phenanthridines and isoquinolines. The use of butyronitrile as the solvent is determinant to the success of the domino pr ...
Background: Protein variability can now be studied by measuring high-resolution tolerance-to-substitution maps and fitness landscapes in saturated mutational libraries. But these rich and expensive datasets are typically interpreted coarsely, restricting d ...
Background: The HIV-1 genome is subject to pressures that target the virus resulting in escape and adaptation. On the other hand, there is a requirement for sequence conservation because of functional and structural constraints. Mapping the sites of select ...
The current state of the art in RDF Stream Processing (RSP) proposes several models and implementations to combine Semantic Web technologies with Data Stream Management System (DSMS) operators like windows. Meanwhile, only a few solutions combine Semantic ...
Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform a detailed analysis of how potassium ions interact with the double helix. The oligomers studied ...
Condition surveying is essential before rehabilitation and modification of a structure. It implies information collection and analysis for structural performance evaluation. Common condition surveying often requires obstructive and invasive techniques that ...
The replication of Moloney murine leukaemia virus relies on the formation of a stable homodimeric 'kissing complex' of a GACG tetraloop interacting through only two C center dot G base pairs flanked of 5'-adjacent Unpaired adenosines A9. Previous NMR inves ...