(Q30359537)

23 September 2017

Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures. (English)

1 reference

23 September 2017

2

Arlo Randall

1 reference

23 September 2017

3

Pierre Baldi

1 reference

23 September 2017

Ken Nagata

1

1 reference

PMC publication ID

4058938

23 September 2017

language of work or name

English

0 references

publication date

25 February 2014

1 reference

23 September 2017

1 reference

23 September 2017

30

1 reference

23 September 2017

12

1 reference

23 September 2017

1681-1689

1 reference

AMS 4.0: consensus prediction of post-translational modifications in protein sequences

23 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

A protein-dependent side-chain rotamer library.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Open Babel: An open chemical toolbox

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

RASP: rapid modeling of protein side chain conformations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Fast and accurate prediction of protein side-chain conformations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

The Dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

PHOSIDA 2011: the posttranslational modification database

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Phospho.ELM: a database of phosphorylation sites--update 2011

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Improved prediction of protein side-chain conformations with SCWRL4

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Expanding the genetic code for biological studies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Prediction of glycosylation sites using random forests

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Human Protein Reference Database--2009 update

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

OPUS-Rota: a fast and accurate method for side-chain modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

A novel method for high accuracy sumoylation site prediction from protein sequences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Adding amino acids to the genetic repertoire

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

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=4058938

The penultimate rotamer library

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Sequence and structure-based prediction of eukaryotic protein phosphorylation sites

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Comparative protein modelling by satisfaction of spatial restraints

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4058938

Expanding molecular modeling and design tools to non-natural sidechains

3 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTU106

Prediction of phosphorylation sites using SVMs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTU106

Predicting O-glycosylation sites in mammalian proteins by using SVMs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTU106

Improved prediction of lysine acetylation by support vector machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTU106

Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTU106

Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTU106

10.1093/BIOINFORMATICS/BTU106

21 January 2018

Identifiers

DOI

1 reference

journals/bioinformatics/NagataRB14

23 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

4058938

23 September 2017

PubMed publication ID

24574112

1 reference

PMC publication ID

4058938