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» Thermodynamics of RNA-RNA Binding
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BMCBI
2010
148views more  BMCBI 2010»
13 years 11 months ago
Analysis of interactions between ribosomal proteins and RNA structural motifs
Background: One important goal of structural bioinformatics is to recognize and predict the interactions between protein binding sites and RNA. Recently, a comprehensive analysis ...
Giovanni Ciriello, Claudio Gallina, Concettina Gue...
JCC
2011
87views more  JCC 2011»
13 years 5 months ago
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations
Abstract: With today’s available computer power, free energy calculations from equilibrium molecular dynamics simulations “via counting” become feasible for an increasing num...
Djurre H. De Jong, Lars V. Schäfer, Alex H. D...
BMCBI
2006
113views more  BMCBI 2006»
13 years 11 months ago
GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima
Background: Computational discovery of transcription factor binding sites (TFBS) is a challenging but important problem of bioinformatics. In this study, improvement of a Gibbs sa...
Kazuhito Shida
BMCBI
2007
94views more  BMCBI 2007»
13 years 11 months ago
A structural analysis of in vitro catalytic activities of hammerhead ribozymes
Background: Ribozymes are small catalytic RNAs that possess the dual functions of sequencespecific RNA recognition and site-specific cleavage. Trans-cleaving ribozymes can inhibit...
Yu Shao, Susan Wu, Chi Yu Chan, Jessie R. Klapper,...
BMCBI
2007
169views more  BMCBI 2007»
13 years 11 months ago
Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and i
Background: Gene expression microarray and other multiplex data hold promise for addressing the challenges of cellular complexity, refined diagnoses and the discovery of well-targ...
Abdallah Sayyed-Ahmad, Kagan Tuncay, Peter J. Orto...