(Q30397719)

25 September 2017

Protein structure determination using metagenome sequence data (English)

1 reference

protein structure determination

25 September 2017

0 references

0 references

author

Nikos C. Kyrpides

8

1 reference

PubMed publication ID

21 June 2017

3

Neha Varghese

0 references

Po-Ssu Huang

object named as

Po-Ssu Huang

4

0 references

David Baker

object named as

David Baker

9

0 references

Hetunandan Kamisetty

7

object named as

Hetunandan Kamisetty

1 reference

25 September 2017

2

Hahnbeom Park

1 reference

25 September 2017

Sergey Ovchinnikov

1

1 reference

25 September 2017

Georgios A Pavlopoulos

5

1 reference

25 September 2017

David E Kim

6

1 reference

25 September 2017

language of work or name

English

0 references

publication date

1 January 2017

1 reference

25 September 2017

1 reference

25 September 2017

355

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25 September 2017

6322

1 reference

25 September 2017

294-298

1 reference

Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Structural basis for amino acid export by DMT superfamily transporter YddG

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Structural basis of lipoprotein signal peptidase II action and inhibition by the antibiotic globomycin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Crystal structure of E. coli lipoprotein diacylglyceryl transferase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

The Pfam protein families database: towards a more sustainable future

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Crystal structures of a double-barrelled fluoride ion channel

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Large-scale determination of previously unsolved protein structures using evolutionary information

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

3Dmol.js: molecular visualization with WebGL.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Sequence co-evolution gives 3D contacts and structures of protein complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

A structural model of the active ribosome-bound membrane protein insertase YidC

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

IMG/M 4 version of the integrated metagenome comparative analysis system

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Improved low-resolution crystallographic refinement with Phenix and Rosetta

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

High-resolution comparative modeling with RosettaCM.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Protein structure prediction from sequence variation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Genomics-aided structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Three-dimensional structures of membrane proteins from genomic sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

The Protein Structure Initiative: achievements and visions for the future

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Protein 3D structure computed from evolutionary sequence variation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

D³: Data-Driven Documents

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

A bioinformatician's guide to metagenomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Data growth and its impact on the SCOP database: new developments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Protein homology detection by HMM-HMM comparison

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Scoring function for automated assessment of protein structure template quality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Protein structure comparison using iterated double dynamic programming

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5493203

Learning generative models for protein fold families.

20 June 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

A new generation of homology search tools based on probabilistic inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

Identification of common molecular subsequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

Fast overlapping of protein contact maps by alignment of eigenvectors

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

A simple and fast heuristic for protein structure comparison.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

A general method applicable to the search for similarities in the amino acid sequence of two proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

MRFalign: protein homology detection through alignment of Markov random fields

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

One contact for every twelve residues allows robust and accurate topology-level protein structure modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

PISCES: a protein sequence culling server

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

The origin of consistent protein structure refinement from structural averaging.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

Discriminative modelling of context-specific amino acid substitution probabilities

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.AAH4043

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28104891

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1126/SCIENCE.AAH4043

1 reference

25 September 2017

1 reference

25 September 2017

PubMed publication ID

28104891

1 reference