Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA-mRNA Complex Recognition Process

Free-Energy Simulations Reveal that Both Hydrophobic and Polar Interactions Are Important for Influenza Hemagglutinin Antibody Binding

(2012) Zhen Xia et al.   BIOPHYSICAL JOURNAL

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

(2011) Elizabeth J. Denning et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system

(2010) S. Kumar et al.   IBM JOURNAL OF RESEARCH AND DEVELOPMENT

Designing small multiple-target artificial RNAs

(2010) Vincent De Guire et al.   NUCLEIC ACIDS RESEARCH

Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis

(2010) Yonghua Wang et al.   PLoS Computational Biology

Recognition Mechanism of siRNA by Viral p19 Suppressor of RNA Silencing: A Molecular Dynamics Study

(2009) Zhen Xia et al.   BIOPHYSICAL JOURNAL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes

(2009) Yanli Wang et al.   NATURE

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Biogenesis of small RNAs in animals

(2009) V. Narry Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Atomic Detail Investigation of the Structure and Dynamics of DNA•RNA Hybrids:  A Molecular Dynamics Study

(2008) U. Deva Priyakumar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex

(2008) Yanli Wang et al.   NATURE

Structure of the guide-strand-containing argonaute silencing complex

(2008) Yanli Wang et al.   NATURE

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS

A method for the analysis of domain movements in large biomolecular complexes

(2008) Guru Prasad Poornam et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS