Related references
Note: Only part of the references are listed.MicroRNA Nanotherapeutics for Lung Targeting. Insights into Pulmonary Hypertension
Susana Carregal-Romero et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)
Alchemical free energy calculations via metadynamics: Application to the theophylline-RNA aptamer complex
Yoshiaki Tanida et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2020)
Repulsive Soft-Core Potentials for Efficient Alchemical Free Energy Calculations
Yaozong Li et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery
Tai-Sung Lee et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides
Melissa C. Hopfinger et al.
NUCLEIC ACIDS RESEARCH (2020)
Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data
Shimpei Nishida et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2019)
Fitting Corrections to an RNA Force Field Using Experimental Data
Andrea Cesari et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
N6-Methyladenosine (m6A): A Promising New Molecular Target in Acute Myeloid Leukemia
Zaira Ianniello et al.
FRONTIERS IN ONCOLOGY (2019)
High Oct4 expression: implications in the pathogenesis of neuroblastic tumours
Ezequiel Monferrer et al.
BMC CANCER (2019)
RNA modifications in structure prediction - Status quo and future challenges
Andrea Tanzer et al.
METHODS (2019)
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Jiri Sponer et al.
CHEMICAL REVIEWS (2018)
Exploring RNA structure and dynamics through enhanced sampling simulations
Vojtech Mlynsky et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)
RNA N6-methyladenosine methyltransferase-like 3 promotes liver cancer progression through YTHDF2-dependent posttranscriptional silencing of SOCS2
Mengnuo Chen et al.
HEPATOLOGY (2018)
Uncertainty Quantification in Alchemical Free Energy Methods
Agastya P. Bhati et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations
Sandro Bottaro et al.
SCIENCE ADVANCES (2018)
m6A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer
Jun Liu et al.
NATURE CELL BIOLOGY (2018)
Selecting New RNA Crystal Contacts
Anastassia Gomez et al.
STRUCTURE (2018)
Stability of RNA duplexes containing inosine•cytosine pairs
Daniel J. Wright et al.
NUCLEIC ACIDS RESEARCH (2018)
METTL14 Suppresses the Metastatic Potential of Hepatocellular Carcinoma by Modulating N6-Methyladenosine- Dependent Primary MicroRNA Processing
Jin-Zhao Ma et al.
HEPATOLOGY (2017)
Post-transcriptional gene regulation by mRNA modifications
Boxuan Simen Zhao et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)
Chemical and structural effects of base modifications in messenger RNA
Emily M. Harcourt et al.
NATURE (2017)
Detecting RNA modifications in the epitranscriptome: predict and validate
Mark Helm et al.
NATURE REVIEWS GENETICS (2017)
N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis
Raghu R. Edupuganti et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)
N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis
Raghu R. Edupuganti et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)
Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function
Ville Y. P. Vaere et al.
BIOMOLECULES (2017)
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
Petra Kuhrova et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
RNA folding pathways in stop motion
Sandro Bottaro et al.
NUCLEIC ACIDS RESEARCH (2016)
Free-energy landscape of a hyperstable RNA tetraloop
Jacob C. Miner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Blind tests of RNA nearest-neighbor energy prediction
Fang-Chieh Chou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells
Gianluigi Lichinchi et al.
NATURE MICROBIOLOGY (2016)
Guidelines for the analysis of free energy calculations
Pavel V. Klimovich et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2015)
Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations
Shun Sakuraba et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2015)
Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification
Caroline Roost et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells
Ayal Hendel et al.
NATURE BIOTECHNOLOGY (2015)
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies
Mohit Chawla et al.
NUCLEIC ACIDS RESEARCH (2015)
The importance of being modified: an unrealized code to RNA structure and function
Paul F. Agris
RNA (2015)
Exometabolom analysis of breast cancer cell lines: Metabolic signature
Lucas Willmann et al.
SCIENTIFIC REPORTS (2015)
Novel Fusion Transcripts Associate with Progressive Prostate Cancer
Yan P. Yu et al.
AMERICAN JOURNAL OF PATHOLOGY (2014)
MeCP2 Suppresses Nuclear MicroRNA Processing and Dendritic Growth by Regulating the DGCR8/Drosha Complex
Tian-Lin Cheng et al.
DEVELOPMENTAL CELL (2014)
Failure to Replicate Depletion of Self-Control
Xiaomeng Xu et al.
PLOS ONE (2014)
Role of tRNA modifications in human diseases
Adrian Gabriel Torres et al.
TRENDS IN MOLECULAR MEDICINE (2014)
Computer Folding of RNA Tetraloops? Are We There Yet?
Petra Kuehrova et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Structure and Function of Noncanonical Nucleobases
Thomas Carell et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2012)
FTO, RNA epigenetics and epilepsy
Joie Rowles et al.
EPIGENETICS (2012)
Silencing microRNA-134 produces neuroprotective and prolonged seizure-suppressive effects
Eva M. Jimenez-Mateos et al.
NATURE MEDICINE (2012)
ViennaRNA Package 2.0
Ronny Lorenz et al.
ALGORITHMS FOR MOLECULAR BIOLOGY (2011)
Free Energy Profile of RNA Hairpins: A Molecular Dynamics Simulation Study
Nan-Jie Deng et al.
BIOPHYSICAL JOURNAL (2010)
Protein Thermostability Calculations Using Alchemical Free Energy Simulations
Daniel Seeliger et al.
BIOPHYSICAL JOURNAL (2010)
RNAstructure: software for RNA secondary structure prediction and analysis
Jessica S. Reuter et al.
BMC BIOINFORMATICS (2010)
Folding of a Small RNA Hairpin Based on Simulation with Replica Exchange Molecular Dynamics
Guanghong Zuo et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics
Allison J. DePaul et al.
NUCLEIC ACIDS RESEARCH (2010)
Conformational Transition Map of an RNA GCAA Tetraloop Explored by Replica-Exchange Molecular Dynamics Simulation
Yufen Zhang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Free energy calculation of modified base-pair formation in explicit solvent: A predictive model
Franck A. P. Vendeix et al.
RNA (2009)
Statistically optimal analysis of samples from multiple equilibrium states
Michael R. Shirts et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Molecular dynamics simulation of the structure, dynamics, and thermostability of the RNA hairpins uCACGg and cUUCGg
Alessandra Villa et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin
Angel E. Garcia et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations
Thomas Steinbrecher et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Molecular dynamics and free energy study of the conformational equilibria in the UUUU RNA hairpin
Nan-Jie Deng et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
AMBER force field parameters for the naturally occurring modified nucleosides in RNA
Raviprasad Aduri et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Nearest neighbor parameters for Inosine•Uridine pairs in RNA duplexes
Daniel J. Wright et al.
BIOCHEMISTRY (2007)
Modified replica exchange simulation methods for local structure refinement
XL Cheng et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
DH Mathews et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
UCSF chimera - A visualization system for exploratory research and analysis
EF Pettersen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Stability and structure of RNA duplexes containing isoguanosine and isocytidine
XY Chen et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)
Experimental and computational studies of the G[UUCG]C RNA tetraloop
DJ Williams et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
Share Paper
