Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB (Q41642027)

6 October 2017

Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB (English)

1 reference

6 October 2017

computational biology

1 reference

inferred from title

author

Mercedes Alfonso-Prieto

object named as

Mercedes Alfonso-Prieto

2

0 references

Michael L. Klein

5

object named as

Michael L Klein

1 reference

6 October 2017

Samridhdi Paudyal

1

1 reference

6 October 2017

Vincenzo Carnevale

3

1 reference

6 October 2017

Shiv K Redhu

4

1 reference

6 October 2017

Allen W Nicholson

6

1 reference

6 October 2017

language of work or name

English

0 references

publication date

21 January 2015

1 reference

6 October 2017

14

1 reference

inferred from page(s)

published in

Proteins

1 reference

6 October 2017

83

1 reference

6 October 2017

459-472

1 reference

6 October 2017

3

1 reference

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Hot-spot analysis to dissect the functional protein-protein interface of a tRNA-modifying enzyme

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Deciphering key features in protein structures with the new ENDscript server

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

RNase III: Genetics and function; structure and mechanism

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Molecular simulations of a dynamic protein complex: role of salt-bridges and polar interactions in configurational transitions

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase III modulator

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Ribonuclease III mechanisms of double-stranded RNA cleavage

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Exploring volatile general anesthetic binding to a closed membrane-bound bacterial voltage-gated sodium channel via computation

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Scalable web services for the PSIPRED Protein Analysis Workbench.

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Moonlighting is mainstream: paradigm adjustment required

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Dynamics in transient complexes of redox proteins

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

RNA-Seq and RNA immunoprecipitation analyses of the transcriptome of Streptomyces coelicolor identify substrates for RNase III

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Parallel Generalized Born Implicit Solvent Calculations with NAMD.

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Xwalk: computing and visualizing distances in cross-linking experiments

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

HMMER web server: interactive sequence similarity searching

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

The macro domain protein family: structure, functions, and their potential therapeutic implications

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

BINANA: a novel algorithm for ligand-binding characterization

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

The critical role of RNA processing and degradation in the control of gene expression.

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

MolProbity: all-atom structure validation for macromolecular crystallography

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

The courtship of proteins: understanding the encounter complex

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Maturation and degradation of ribosomal RNA in bacteria

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Identification of hot-spot residues in protein-protein interactions by computational docking

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

How well can the accuracy of comparative protein structure models be predicted?

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

A stepwise model for double-stranded RNA processing by ribonuclease III

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Version 1.2 of the Crystallography and NMR system

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Maturation and degradation of RNA in bacteria

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Structural basis for non-catalytic and catalytic activities of ribonuclease III.

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Degradation of RNA in bacteria: comparison of mRNA and stable RNA

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

WHISCY: what information does surface conservation yield? Application to data-driven docking.

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Scalable molecular dynamics with NAMD

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1 A

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Structural disorder throws new light on moonlighting

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Data-driven docking: HADDOCK's adventures in CAPRI.

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

The FoldX web server: an online force field

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

The macro domain is an ADP-ribose binding module

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Anchor residues in protein-protein interactions

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

WebLogo: A Sequence Logo Generator

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Structure and Substrate Binding Properties of cobB, a Sir2 Homolog Protein Deacetylase from Escherichia coli

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Protein structure prediction and structural genomics

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Electrostatics of nanosystems: application to microtubules and the ribosome

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Modeling of loops in protein structures

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Anatomy of hot spots in protein interfaces

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

RNase III autoregulation: structure and function of rncO, the posttranscriptional "operator"

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

VMD: visual molecular dynamics

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Comparative protein modelling by satisfaction of spatial restraints

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Autoregulation of RNase III operon by mRNA processing

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Sequence logos: a new way to display consensus sequences

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

On the use of structural templates for high-resolution docking.

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Intermediate states of ribonuclease III in complex with double-stranded RNA.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Defining the limits of homology modeling in information-driven protein docking.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

"Fuzziness" in the celular interactome: a historical perspective.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

MODBASE, a database of annotated comparative protein structure models and associated resources.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Computational alanine scanning of protein-protein interfaces

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Identification of protein-protein interaction sites from docking energy landscapes.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

Escherichia coli ribonuclease III: affinity purification of hexahistidine-tagged enzyme and assays for substrate binding and cleavage

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4329070

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

18 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.24751

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.24751

Expression and characterization of RNase III and Era proteins. Products of the rnc operon of Escherichia coli

21 January 2018

1 reference

12 December 2020

10Sa RNA: processing by and inhibition of RNase III

1 reference

12 December 2020

RNase III cleavages in non-coding leaders of Escherichia coli transcripts control mRNA stability and genetic expression

1 reference

12 December 2020

RNase III is positively regulated by T7 protein kinase

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.24751

1 reference

6 October 2017

1 reference

6 October 2017

1 reference