(Q30378725)

12 August 2017

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

1 reference

12 August 2017

Sergey Ovchinnikov

1

0 references

David Baker

object named as

David Baker

9

0 references

Nick Grishin

8

object named as

Nick V Grishin

1 reference

12 August 2017

7

Hetunandan Kamisetty

1 reference

12 August 2017

3

Hahnbeom Park

1 reference

12 August 2017

Lisa Kinch

2

1 reference

12 August 2017

Yuxing Liao

4

1 reference

12 August 2017

Jimin Pei

5

1 reference

12 August 2017

David E Kim

6

1 reference

12 August 2017

language of work or name

English

0 references

publication date

3 September 2015

1 reference

12 August 2017

1 reference

12 August 2017

4

1 reference

12 August 2017

e09248

1 reference

Ocean plankton. Structure and function of the global ocean microbiome

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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=4602095

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=4602095

Analysis of two domains with novel RNA-processing activities throws light on the complex evolution of ribosomal RNA biogenesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Expanded microbial genome coverage and improved protein family annotation in the COG database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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=4602095

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=4602095

Conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous 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=4602095

Proposed carrier lipid-binding site of undecaprenyl pyrophosphate phosphatase from Escherichia coli

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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=4602095

Inverted topologies in membrane proteins: a mini-review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Mechanism of farnesylated CAAX protein processing by the intramembrane protease Rce1

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Activities at the Universal Protein Resource (UniProt)

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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=4602095

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=4602095

A two-domain elevator mechanism for sodium/proton antiport

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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=4602095

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=4602095

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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=4602095

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=4602095

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=4602095

Phosphatidylglycerol::prolipoprotein diacylglyceryl transferase (Lgt) of Escherichia coli has seven transmembrane segments, and its essential residues are embedded in the membrane

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Antiparallel EmrE exports drugs by exchanging between asymmetric structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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=4602095

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=4602095

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=4602095

Benchmarking and analysis of protein docking performance in Rosetta v3.2.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

The cytochrome bd respiratory 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=4602095

CREST--a large and diverse superfamily of putative transmembrane hydrolases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Improved molecular replacement by density- and energy-guided protein structure optimization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

A new generation of homology search tools based on probabilistic inference

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Structure prediction for CASP8 with all-atom refinement using 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=4602095

Macromolecular modeling with 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=4602095

Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

The structure of membrane associated proteins in eicosanoid and glutathione metabolism as determined by electron crystallography.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

UniRef: comprehensive and non-redundant UniProt reference clusters

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Discontinuous membrane helices in transport proteins and their correlation with function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Quasi-symmetry in the cryo-EM structure of EmrE provides the key to modeling its transmembrane domain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Evidence for a novel protease governing regulated intramembrane proteolysis and resistance to antimicrobial peptides in Bacillus subtilis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Lipid-protein interactions in double-layered two-dimensional AQP0 crystals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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=4602095

Structure of a glutamate transporter homologue from Pyrococcus horikoshii

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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=4602095

Protein structure prediction using 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=4602095

PISCES: a protein sequence culling server

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Effective energy function for proteins in solution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Common structural features of MAPEG -- a widespread superfamily of membrane associated proteins with highly divergent functions in eicosanoid and glutathione metabolism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Crystal structures of aconitase with trans-aconitate and nitrocitrate bound

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Amino acid preferences at protein binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Molecules as documents of evolutionary history

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4602095

Learning generative models for protein fold families.

20 June 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.09248

Identification of multiple genes encoding membrane proteins with undecaprenyl pyrophosphate phosphatase (UppP) activity in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.09248

The integral membrane FtsW protein and peptidoglycan synthase PBP3 form a subcomplex in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.09248

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

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.09248

SATP (YaaH), a succinate-acetate transporter protein in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.09248

Tara Oceans studies plankton at planetary scale

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.09248

GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.09248

Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.09248

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/26335199

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identification and evolution of dual-topology membrane proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26335199

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identification of the L-tartrate dehydratase genes (ttdA and ttdB) of Escherichia coli and evolutionary relationship with the class I fumarase genes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26335199

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.7554/ELIFE.09248

1 reference

12 August 2017

1 reference

12 August 2017

PubMed publication ID

26335199

1 reference