RNA and protein 3D structure modeling: similarities and differences

RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA

(2012) Hugo M. Martinez et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Free Energy Profile of RNA Hairpins: A Molecular Dynamics Simulation Study

(2010) Nan-Jie Deng et al.   BIOPHYSICAL JOURNAL

Folding of a Small RNA Hairpin Based on Simulation with Replica Exchange Molecular Dynamics

(2010) Guanghong Zuo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures

(2010) Zhen Xia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA

(2010) Samuela Pasquali et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

Predicting loop-helix tertiary structural contacts in RNA pseudoknots

(2010) S. Cao et al.   RNA

On the significance of an RNA tertiary structure prediction

(2010) C. E. Hajdin et al.   RNA

A New Computational Approach for Mechanical Folding Kinetics of RNA Hairpins

(2009) Song Cao et al.   BIOPHYSICAL JOURNAL

Limitations of Induced Folding in Molecular Recognition by Intrinsically Disordered Proteins

(2009) Eszter Hazy et al.   CHEMPHYSCHEM

CHARMM: The biomolecular simulation program

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

Constraint counting on RNA structures: Linking flexibility and function

(2009) Simone Fulle et al.   METHODS

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

Evaluation of template-based models in CASP8 with standard measures

(2009) Domenico Cozzetto et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction-Round VIII

(2009) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of CASP8 structure predictions for template free targets

(2009) Moshe Ben-David et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

(2009) M. A. Jonikas et al.   RNA

New metrics for comparing and assessing discrepancies between RNA 3D structures and models

(2009) M. Parisien et al.   RNA

Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain

(2008) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics

(2008) Joanna Sarzyńska et al.   BIOPOLYMERS

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

(2008) F. Ding et al.   RNA

Understanding the molecular machinery of genetics through 3D structures

(2007) Roman A. Laskowski et al.   NATURE REVIEWS GENETICS