Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state

Aptamers as targeted therapeutics: current potential and challenges

(2016) Jiehua Zhou et al.   NATURE REVIEWS DRUG DISCOVERY

FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs

(2015) Maxwell I. Zimmerman et al.   Journal of Chemical Theory and Computation

Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps

(2015) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis

(2015) Pablo Cordero et al.   PLoS Computational Biology

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

(2014) Matteo Salvalaglio et al.   Journal of Chemical Theory and Computation

Complex RNA Folding Kinetics Revealed by Single-Molecule FRET and Hidden Markov Models

(2014) Bettina G. Keller et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

(2014) Maciej Antczak et al.   NUCLEIC ACIDS RESEARCH

Aptamers: Molecules of great potential

(2013) Filip Radom et al.   BIOTECHNOLOGY ADVANCES

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

From Metadynamics to Dynamics

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW LETTERS

RNA-Based Therapeutics: Current Progress and Future Prospects

(2012) John C. Burnett et al.   CHEMISTRY & BIOLOGY

Therapeutic RNA aptamers in clinical trials

(2012) Padma Sundaram et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

(2012) Gregory R. Bowman   JOURNAL OF CHEMICAL PHYSICS

EMMA: A Software Package for Markov Model Building and Analysis

(2012) Martin Senne et al.   Journal of Chemical Theory and Computation

Selective transformations of complex molecules are enabled by aptameric protective groups

(2012) Andreas A. Bastian et al.   Nature Chemistry

Simple few-state models reveal hidden complexity in protein folding

(2012) K. A. Beauchamp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aptamer Modules as Sensors and Detectors

(2011) Michael Famulok et al.   ACCOUNTS OF CHEMICAL RESEARCH

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations

(2011) Weihua Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables

(2011) Jan-Hendrik Prinz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Daunomycin interaction with DNA: Microcalorimetric studies of the thermodynamics and binding mechanism

(2010) Po-Hsun Lin et al.   Biotechnology Journal

g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

(2010) Jochen S. Hub et al.   Journal of Chemical Theory and Computation

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Aptamers as therapeutics

(2010) Anthony D. Keefe et al.   NATURE REVIEWS DRUG DISCOVERY

Design Strategies for Aptamer-Based Biosensors

(2010) Kun Han et al.   SENSORS

Aptamers Generated from Cell-SELEX for Molecular Medicine: A Chemical Biology Approach

(2009) Xiaohong Fang et al.   ACCOUNTS OF CHEMICAL RESEARCH

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

NMR Chemical Exchange as a Probe for Ligand-Binding Kinetics in a Theophylline-Binding RNA Aptamer

(2009) Michael P. Latham et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA dynamics: it is about time

(2008) Hashim M Al-Hashimi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Probability distributions of molecular observables computed from Markov models

(2008) Frank Noé   JOURNAL OF CHEMICAL PHYSICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

A temperature predictor for parallel tempering simulations

(2008) Alexandra Patriksson et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation

The implementation of a fast and accurate QM/MM potential method in Amber

(2007) Ross C. Walker et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY