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ECCC
2010
82views more  ECCC 2010»
13 years 10 months ago
On optimal proof systems and logics for PTIME
We prove that TAUT has a p-optimal proof system if and only if a logic related to least fixed-point logic captures polynomial time on all finite structures. Furthermore, we show t...
Yijia Chen, Jörg Flum
BMCBI
2010
86views more  BMCBI 2010»
13 years 10 months ago
Mining protein loops using a structural alphabet and statistical exceptionality
Background: Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, ca...
Leslie Regad, Juliette Martin, Grégory Nuel...
BMCBI
2010
205views more  BMCBI 2010»
13 years 10 months ago
A fast indexing approach for protein structure comparison
Background: Protein structure comparison is a fundamental task in structural biology. While the number of known protein structures has grown rapidly over the last decade, searchin...
Lei Zhang, James Bailey, Arun Siddharth Konagurthu...
BMCBI
2006
121views more  BMCBI 2006»
13 years 10 months ago
Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using
Background: Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models h...
Yadhu Kumar, Ralf Westram, Peter Kipfer, Harald Me...
WABI
2010
Springer
128views Bioinformatics» more  WABI 2010»
13 years 8 months ago
Sparsification of RNA Structure Prediction Including Pseudoknots
Background: Although many RNA molecules contain pseudoknots, computational prediction of pseudoknotted RNA structure is still in its infancy due to high running time and space con...
Mathias Möhl, Raheleh Salari, Sebastian Will,...