pH-dependent dynamics of complex RNA macromolecules (Q36697118)

15 August 2017

pH-dependent dynamics of complex RNA macromolecules (English)

1 reference

15 August 2017

1 reference

Garrett B Goh

1

1 reference

15 August 2017

Jennifer L Knight

series ordinal

2

1 reference

15 August 2017

Charles L Brooks

series ordinal

3

1 reference

15 August 2017

3 January 2013

1 reference

Journal of Chemical Theory and Computation

15 August 2017

1 reference

15 August 2017

9

1 reference

15 August 2017

2

1 reference

15 August 2017

935-943

1 reference

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Unraveling A Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

pH-replica exchange molecular dynamics in proteins using a discrete protonation method

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Multisite λ Dynamics for Simulated Structure–Activity Relationship Studies

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Probing pH-Dependent Dissociation of HdeA Dimers

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

The pKa Cooperative: A collaborative effort to advance structure‐based calculations of pKa values and electrostatic effects in proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

pH replica‐exchange method based on discrete protonation states

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

An active-site guanine participates in glmS ribozyme catalysis in its protonated state

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Applying efficient implicit nongeometric constraints in alchemical free energy simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Charged Nucleobases and Their Potential for RNA Catalysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Predicting pKa Values with Continuous Constant pH Molecular Dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

The pH Dependence of Hairpin Ribozyme Catalysis Reflects Ionization of an Active Site Adenine

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H forms are most consistent with crystal structures of hairpin ribozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

CHARMM: the biomolecular simulation program

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

λ-Dynamics free energy simulation methods

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Computations of standard binding free energies with molecular dynamics simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Linking folding with aggregation in Alzheimer's beta-amyloid peptides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

The ribosomal peptidyl transferase

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Structural roles of monovalent cations in the HDV ribozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Exploring atomistic details of pH-dependent peptide folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Toward the accurate first-principles prediction of ionization equilibria in proteins.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Role of an active site adenine in hairpin ribozyme catalysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Constant pH molecular dynamics with proton tautomerism

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Free energy calculations and ligand binding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Protonation of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

pH-dependent conformational flexibility within the ribosomal peptidyl transferase center.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

pKa of adenine 2451 in the ribosomal peptidyl transferase center remains elusive

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

A Novel View of pH Titration in Biomolecules†

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

On the truncation of long-range electrostatic interactions in DNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Dynamics of the RNA hairpin GNRA tetraloop

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Stabilization of the anticodon stem-loop of tRNALys,3 by an A -C base-pair and by pseudouridine

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Structure of an RNA internal loop consisting of tandem C-A base pairs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

A network of heterogeneous hydrogen bonds in GNRA tetraloops

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Purine-purine mismatches in RNA helices: evidence for protonated G.A pairs and next-nearest neighbor effects

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops"

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

A CA( ) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Exploration of the conserved A C wobble pair within the ribosomal peptidyl transferase center using affinity purified mutant ribosomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Probing Conformational States of Modified Helix 69 in 50S Ribosomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Uncovering Specific Electrostatic Interactions in the Denatured States of Proteins

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

The pH-dependent conformational states of kyotorphin: a constant-pH molecular dynamics study

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Nucleobase catalysis in the hairpin ribozyme

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Essential mechanisms in the catalysis of peptide bond formation on the ribosome.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Simultaneous escaping of explicit and hidden free energy barriers: application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Acidic range titration of HEWL using a constant-pH molecular dynamics method

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

General acid catalysis by the hepatitis delta virus ribozyme

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Constant pH molecular dynamics in generalized Born implicit solvent

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

A conformational switch controls hepatitis delta virus ribozyme catalysis

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Catalytic roles for proton transfer and protonation in ribozymes

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Generalized born model with a simple smoothing function

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Adenine protonation in domain B of the hairpin ribozyme

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3601751

Molecular simulation with variable protonation states at constant pH

5 September 2018

1 reference

12 December 2020

NMR studies of A.C mismatches in DNA dodecanucleotides at acidic pH. Wobble A(anti).C(anti) pair formation

1 reference

12 December 2020

Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage

1 reference

12 December 2020

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

12 December 2020

The contribution of cytosine protonation to the stability of parallel DNA triple helices 1 1Edited by D. E. Draper

1 reference

12 December 2020

Constant-pH Molecular Dynamics Simulations Reveal a β-Rich Form of the Human Prion Protein

1 reference

12 December 2020

Effects of solute-solvent proton exchange on polypeptide chain dynamics: a constant-pH molecular dynamics study

1 reference

12 December 2020

Order, dynamics and metal-binding in the lead-dependent ribozyme

1 reference

12 December 2020

Energetics of a strongly pH dependent RNA tertiary structure in a frameshifting pseudoknot

1 reference

12 December 2020

Conformational Transition Map of an RNA GCAA Tetraloop Explored by Replica-Exchange Molecular Dynamics Simulation

1 reference

12 December 2020

A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion

1 reference

12 December 2020

Theoretical investigation of the behavior of titratable groups in proteins

1 reference

12 December 2020

Active site dynamics in the lead-dependent ribozyme

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT300942Z

1 reference

15 August 2017

1 reference

15 August 2017

PubMed publication ID

23525495

1 reference