ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules (Q39776544)

14 September 2017

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules (English)

1 reference

14 September 2017

1 reference

6

1 reference

14 September 2017

Haim Ashkenazy

1

0 references

Itay Mayrose

object named as

Itay Mayrose

5

0 references

Nir Ben-Tal

object named as

Nir Ben-Tal

7

0 references

author name string

Shiran Abadi

2

1 reference

14 September 2017

Eric Martz

3

1 reference

14 September 2017

Ofer Chay

4

1 reference

14 September 2017

language of work or name

English

0 references

publication date

10 May 2016

1 reference

14 September 2017

Nucleic Acids Research

1 reference

14 September 2017

44

1 reference

14 September 2017

W1

1 reference

14 September 2017

W344-50

1 reference

Creative Commons Attribution-NonCommercial 4.0 International

14 September 2017

start time

14 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Structural basis of outer membrane protein insertion by the BAM complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

The bacterial dicarboxylate transporter VcINDY uses a two-domain elevator-type mechanism.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Causes of evolutionary rate variation among protein sites

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Protein structure. Structure and activity of tryptophan-rich TSPO proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Rfam 12.0: updates to the RNA families database

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Functional evaluation of autism-associated mutations in NHE9.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

CD-HIT: accelerated for clustering the next-generation sequencing data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

jModelTest 2: more models, new heuristics and parallel computing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

22 September 2017

ViennaRNA Package 2.0

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

ProtTest 3: fast selection of best-fit models of protein evolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

A comparative study of conservation and variation scores

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

INTREPID: a web server for prediction of functionally important residues by evolutionary analysis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Sequence context-specific profiles for homology searching

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

An improved general amino acid replacement matrix

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Inference of macromolecular assemblies from crystalline state

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Did the last common ancestor have a biological membrane?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

The accuracy of several multiple sequence alignment programs for proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

A family of evolution-entropy hybrid methods for ranking protein residues by importance.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Importance of the reverse Hoogsteen base pair 54-58 for tRNA function

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Scoring residue conservation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Prediction of coordination number and relative solvent accessibility in proteins.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

22 September 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=4987940

Twilight zone of protein sequence alignments

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

An evolutionary trace method defines binding surfaces common to protein families

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Comparative protein modelling by satisfaction of spatial restraints

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Basic local alignment search tool

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

The rapid generation of mutation data matrices from protein sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Computational identification of natural peptides based on analysis of molecular evolution

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Detection of functionally important regions in "hypothetical proteins" of known structure

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Predicting functionally important residues from sequence conservation.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

A gamma mixture model better accounts for among site rate heterogeneity

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

In silico identification of functional regions in proteins.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

ConSeq: the identification of functionally and structurally important residues in protein sequences.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Selecting the best-fit model of nucleotide substitution.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

A fast method to predict protein interaction sites from sequences

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

Identification of functional surfaces of the zinc binding domains of intracellular receptors

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4987940

ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function

20 August 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW408

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW408

Selecting the Best-Fit Model of Nucleotide Substitution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW408

A new look at the statistical model identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW408

JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW408

Site-Specific Evolutionary Rate Inference: Taking Phylogenetic Uncertainty into Account

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW408

Automatic methods for predicting functionally important residues

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27166375

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Model of amino acid substitution in proteins encoded by mitochondrial DNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27166375

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKW408

1 reference

journals/nar/AshkenazyAMCMPB16

14 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

14 September 2017

1 reference