ECOD: an evolutionary classification of protein domains. (Q30369391)

13 November 2017

ECOD: an evolutionary classification of protein domains. (English)

1 reference

13 November 2017

2

R Dustin Schaeffer

1 reference

PubMed publication ID

21 June 2017

8

Nick V Grishin

1 reference

13 November 2017

7

Bong-Hyun Kim

1 reference

13 November 2017

Hua Cheng

1

1 reference

13 November 2017

Yuxing Liao

3

1 reference

13 November 2017

Lisa N Kinch

4

1 reference

13 November 2017

Jimin Pei

5

1 reference

13 November 2017

Shuoyong Shi

6

1 reference

13 November 2017

4 December 2014

1 reference

PLOS Computational Biology

13 November 2017

1 reference

13 November 2017

10

1 reference

13 November 2017

12

1 reference

13 November 2017

e1003926

1 reference

Creative Commons Attribution 4.0 International

13 November 2017

start time

4 December 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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SCOP2 prototype: a new approach to protein structure mining

3 June 2018

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Structural basis for molecular recognition of folic acid by folate receptors

3 June 2018

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Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

3 June 2018

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S-adenosyl-methionine-dependent methyltransferases: highly versatile enzymes in biocatalysis, biosynthesis and other biotechnological applications.

3 June 2018

1 reference

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Cysteine-rich domains related to Frizzled receptors and Hedgehog-interacting proteins

3 June 2018

1 reference

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Crystal Structure of N -Glycosylated Human Glypican-1 Core Protein

3 June 2018

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3 June 2018

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Structure of the protein core of the glypican Dally-like and localization of a region important for hedgehog signaling

3 June 2018

1 reference

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CDD: a Conserved Domain Database for the functional annotation of proteins

3 June 2018

1 reference

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BLAST : architecture and applications

3 June 2018

1 reference

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Crystal Structure of the Frizzled-Like Cysteine-Rich Domain of the Receptor Tyrosine Kinase MuSK

3 June 2018

1 reference

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The GD box: a widespread noncontiguous supersecondary structural element

3 June 2018

1 reference

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Structure of N-Terminal Domain of NPC1 Reveals Distinct Subdomains for Binding and Transfer of Cholesterol

3 June 2018

1 reference

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HorA web server to infer homology between proteins using sequence and structural similarity.

3 June 2018

1 reference

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Cradle-loop barrels and the concept of metafolds in protein classification by natural descent.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets

3 June 2018

1 reference

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Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

NAD metabolism in health and disease

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

BLAST: improvements for better sequence analysis

3 June 2018

1 reference

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The HHpred interactive server for protein homology detection and structure prediction

3 June 2018

1 reference

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AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

TM-align: a protein structure alignment algorithm based on the TM-score

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

The many faces of the helix-turn-helix domain: transcription regulation and beyond

3 June 2018

1 reference

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4SCOPmap: automated assignment of protein structures to evolutionary superfamilies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Protein homology detection by HMM-HMM comparison

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

MUSCLE: multiple sequence alignment with high accuracy and high throughput

3 June 2018

1 reference

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The ASTRAL Compendium in 2004

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Cytoscape: a software environment for integrated models of biomolecular interaction networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

More than the sum of their parts: on the evolution of proteins from peptides

3 June 2018

1 reference

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Many paths to methyltransfer: a chronicle of convergence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Features of a Smad3 MH1-DNA complex. Roles of water and zinc in DNA binding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Review: what can structural classifications reveal about protein evolution?

3 June 2018

1 reference

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AL2CO: calculation of positional conservation in a protein sequence alignment.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Insights into Wnt binding and signalling from the structures of two Frizzled cysteine-rich domains

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Mh1 domain of Smad is a degraded homing endonuclease

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

DaliLite workbench for protein structure comparison

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

3 June 2018

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=4256011

A systematic comparison of protein structure classifications: SCOP, CATH and FSSP

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

How far divergent evolution goes in proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

CATH--a hierarchic classification of protein domain structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Crystal structure of chicken riboflavin-binding protein.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

NAD-binding domains of dehydrogenases

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Mapping the protein universe

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Protein structure comparison by alignment of distance matrices

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Why do globular proteins fit the limited set of folding patterns?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256011

Identification of distant homologues of fibroblast growth factors suggests a common ancestor for all β-trefoil proteins 1 1Edited by J. Thornton

3 June 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1003926

Structural ties between cholesterol transport and morphogen signaling

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1003926

PDP: protein domain parser.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1003926

Structurally analogous proteins do exist!

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1003926

Evolution of the beta-propeller fold.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1003926

Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25474468

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003926

1 reference

journals/ploscb/ChengSLKPSKG14

13 November 2017

1 reference

DBLP Dataset 2021-01-02

release_65l7i3zbfzcvxbm6exmyjerrzm

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/65l7i3zbfzcvxbm6exmyjerrzm

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

13 November 2017

PubMed publication ID

25474468

1 reference