Molecular evolution of dihydrouridine synthases (Q34319810)

1 August 2017

title

Molecular evolution of dihydrouridine synthases (English)

1 reference

1 August 2017

3

Janusz M Bujnicki

1 reference

1 August 2017

Joanna M Kasprzak

1

1 reference

1 August 2017

Anna Czerwoniec

series ordinal

2

1 reference

1 August 2017

publication date

28 June 2012

1 reference

1 August 2017

1 reference

1 August 2017

volume

13

1 reference

1 August 2017

page(s)

153

1 reference

MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins

1 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Molecular basis of dihydrouridine formation on tRNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Computational methods for prediction of protein-RNA interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Mechanism of dihydrouridine synthase 2 from yeast and the importance of modifications for efficient tRNA reduction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

MODOMICS: a database of RNA modification pathways. 2008 update

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

MetaMQAP: a meta-server for the quality assessment of protein models.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Prediction of global and local model quality in CASP7 using Pcons and ProQ.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

PrDOS: prediction of disordered protein regions from amino acid sequence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

WoLF PSORT: protein localization predictor

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Locating proteins in the cell using TargetP, SignalP and related tools

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Physically realistic homology models built with ROSETTA can be more accurate than their templates

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Exploiting heterogeneous sequence properties improves prediction of protein disorder.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

A novel human tRNA-dihydrouridine synthase involved in pulmonary carcinogenesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

CLANS: a Java application for visualizing protein families based on pairwise similarity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Protein disorder prediction: implications for structural proteomics

6 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

6 July 2018

https://api.crossref.org/works/10.1186%2F1471-2105-13-153

The COG database: an updated version includes eukaryotes

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

MrBayes 3: Bayesian phylogenetic inference under mixed models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

GeneSilico protein structure prediction meta-server.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Intrinsic disorder and protein function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Pcons: a neural-network-based consensus predictor that improves fold recognition.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Electrostatics of nanosystems: application to microtubules and the ribosome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Compilation of tRNA sequences and sequences of tRNA genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Posttranscriptional modification of tRNA in psychrophilic bacteria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Conformational flexibility in RNA: the role of dihydrouridine

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Comparative protein modelling by satisfaction of spatial restraints

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Posttranscriptional modification of the central loop of domain V in Escherichia coli 23 S ribosomal RNA.

6 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-153

Identification of the tRNA-dihydrouridine synthase family.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-153

Molecular determinants of dihydrouridine synthase activity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-153

The 1.59 A resolution crystal structure of TM0096, a flavin mononucleotide binding protein from Thermotoga maritima

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-153

Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-153

Predicting nuclear localization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-153

POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-153

Prediction of RNA binding sites in a protein using SVM and PSSM profile.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3674756

Inactivation of dihydropyrimidine dehydrogenase by 5-iodouracil

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22741570

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22741570

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-13-153

1 reference

journals/bmcbi/KasprzakCB12

1 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

1 August 2017

1 reference