EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference (Q37708927)

22 August 2017

EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference (English)

1 reference

22 August 2017

3

Jeffrey Skolnick

1 reference

22 August 2017

Weidong Tian

1

1 reference

22 August 2017

Adrian K Arakaki

series ordinal

2

1 reference

22 August 2017

language of work or name

English

0 references

publication date

1 December 2004

1 reference

22 August 2017

Nucleic Acids Research

1 reference

22 August 2017

32

1 reference

22 August 2017

21

1 reference

22 August 2017

6226-6239

1 reference

Identifying latent enzyme activities: substrate ambiguity within modern bacterial sugar kinases

22 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

A structural study for the optimisation of functional motifs encoded in protein sequences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Automatic prediction of protein function

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Enzyme-specific profiles for genome annotation: PRIAM

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Definitions of enzyme function for the structural genomics era.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

PROSITE: a documented database using patterns and profiles as motif descriptors

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Plasticity of enzyme active sites

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

The past, present and future of genome-wide re-annotation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

The Pfam protein families database

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Intrinsic errors in genome annotation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Pathogenesis and evolution of virulence in enteropathogenic and enterohemorrhagic Escherichia coli

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

The ENZYME database in 2000

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

23 August 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

PRINTS-S: the database formerly known as PRINTS.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

KEGG: kyoto encyclopedia of genes and genomes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Flexible sequence similarity searching with the FASTA3 program package

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

From protein structure to function.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Profile hidden Markov models

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Local alignment statistics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

An evolutionary trace method defines binding surfaces common to protein families

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

A method to predict functional residues in proteins

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Glycolate oxidoreductase in Escherichia coli

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Optimal alignments in linear space

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Amino acid substitution matrices from protein blocks

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

23 August 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

23 August 2017

https://api.crossref.org/works/10.1093%2FNAR%2FGKH956

Increased coverage of protein families with the blocks database servers

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

glc locus of Escherichia coli: characterization of genes encoding the subunits of glycolate oxidase and the glc regulator protein

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Predicting functions from protein sequences--where are the bottlenecks?

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity?

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Analysis and prediction of functional sub-types from protein sequence alignments.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=535665

Optimal alignments in linear space

1 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKH956

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKH956

Errors in genome annotation

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15576349

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Defining the mandate of proteomics in the post-genomics era: workshop report

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15576349

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Automatic methods for predicting functionally important residues

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15576349

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKH956

1 reference

22 August 2017

1 reference

22 August 2017

PubMed publication ID

15576349

1 reference