(Q30402159)

15 October 2017

Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation (English)

1 reference

15 October 2017

2

1 reference

15 October 2017

4

Michael Levitt

1 reference

15 October 2017

Julie Bernauer

1

0 references

author name string

Adelene Y L Sim

series ordinal

3

1 reference

PMC publication ID

3096039

15 October 2017

language of work or name

English

0 references

publication date

26 April 2011

1 reference

15 October 2017

1 reference

15 October 2017

17

1 reference

15 October 2017

6

1 reference

15 October 2017

1066-1075

1 reference

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

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Turning limited experimental information into 3D models of RNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Consistent refinement of submitted models at CASP using a knowledge-based potential

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Atomic accuracy in predicting and designing noncanonical RNA structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

A probabilistic model of RNA conformational space

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Classification and energetics of the base-phosphate interactions in RNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Frequency and isostericity of RNA base pairs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Solvent dramatically affects protein structure refinement.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

iFoldRNA: three-dimensional RNA structure prediction and folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Automated de novo prediction of native-like RNA tertiary structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Bridging the gap in RNA structure prediction.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Near-native structure refinement using in vacuo energy minimization.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Beyond Mfold: recent advances in RNA bioinformatics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Revolutions in RNA secondary structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Describing RNA structure by libraries of clustered nucleotide doublets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Extracting stacking interaction parameters for RNA from the data set of native structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

PDB file parser and structure class implemented in Python

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

RNA backbone is rotameric

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

An improved protein decoy set for testing energy functions for protein structure prediction.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Mfold web server for nucleic acid folding and hybridization prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

RNABase: an annotated database of RNA structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

A distance-dependent atomic knowledge-based potential for improved protein structure selection.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Tertiary Motifs in RNA Structure and Folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

New Monte Carlo algorithms for protein folding.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Canonical dynamics: Equilibrium phase-space distributions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Hierarchy and dynamics of RNA folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Basic local alignment search tool

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

RNA secondary structure analysis using the Vienna RNA package.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3096039

Theory and applications of the generalized Born solvation model in macromolecular simulations

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21521828

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21521828

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21521828

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Modeling Unusual Nucleic Acid Structures

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1261/RNA.2543711

Replica-exchange molecular dynamics method for protein folding

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1261/RNA.2543711

Finite Mixture Models

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1261/RNA.2543711

Identifiers

DOI

10.1261/RNA.2543711

1 reference

15 October 2017

1 reference

PMC publication ID

3096039

15 October 2017

PubMed publication ID

21521828

1 reference

PMC publication ID

3096039