Functional classification of protein structures by local structure matching in graph representation. (Q52617091)

http://europepmc.org/abstract/PMC/5980557

18 June 2018

title

Functional classification of protein structures by local structure matching in graph representation. (English)

1 reference

http://europepmc.org/abstract/PMC/5980557

18 June 2018

author

Penny J Beuning

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Joslynn S Lee

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Alexandru Suciu

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

author name string

Caitlyn L Mills

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Rohan Garg

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Liang Tian

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Mary Jo Ondrechen

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

Gene D Cooperman

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

publication date

27 April 2018

1 reference

http://europepmc.org/abstract/PMC/5980557

18 June 2018

published in

Protein Science

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

volume

27

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

page(s)

1125-1135

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases.

9 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Biochemical functional predictions for protein structures of unknown or uncertain function

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Template-based prediction of protein function

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs)

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

The Enzyme Function Initiative

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

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

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

High-performance prediction of functional residues in proteins with machine learning and computed input features.

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Functional classification of protein 3D structures from predicted local interaction sites

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Crystal structure of 3-hexulose-6-phosphate synthase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

The interaction of ammonia and xenon with the imidazole glycerol phosphate synthase from Thermotoga maritima as detected by NMR spectroscopy

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

An overview of in silico protein function prediction.

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Protein function annotation by homology-based inference

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Structure-based function prediction: approaches and applications.

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

BLOSUM62 miscalculations improve search performance

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Predicting protein function from sequence and structure

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Network-based prediction of protein function

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Genes involved in intrinsic antibiotic resistance of Acinetobacter baylyi

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Where did the BLOSUM62 alignment score matrix come from?

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Structure and catalytic mechanism of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Two (betaalpha)(8)-barrel enzymes of histidine and tryptophan biosynthesis have similar reaction mechanisms and common strategies for protecting their labile substrates

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

The catalytic mechanism of indole-3-glycerol phosphate synthase: crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Enzyme function less conserved than anticipated.

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Divergent evolution of (betaalpha)8-barrel enzymes.

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Imidazole glycerol phosphate synthase from Thermotoga maritima. Quaternary structure, steady-state kinetics, and reaction mechanism of the bienzyme complex

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

The structural basis for the remarkable catalytic proficiency of orotidine 5'-monophosphate decarboxylase

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

The crystal structure and mechanism of orotidine 5'-monophosphate decarboxylase

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Crystallographic studies of phosphonate-based alpha-reaction transition-state analogues complexed to tryptophan synthase

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

SCOP: a structural classification of proteins database for the investigation of sequences and structures

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: Indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 Å resolution

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Induction of protective immunity against Burkholderia pseudomallei using attenuated mutants with defects in the intracellular life cycle

18 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: structural basis for catalytic promiscuity in wild-type and designed mutants of 3-keto-L-gulonate 6-phosphate decarboxylase.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: enhancing the promiscuous D-arabino-hex-3-ulose 6-phosphate synthase reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

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

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5980557

13 August 2018

Identifiers

DOI

10.1002/PRO.3416

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29604149%20AND%20SRC:MED&resulttype=core&format=json

9 June 2020

PubMed publication ID

29604149

1 reference