(Q36491558)

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DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications

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scholarly article

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Europe PubMed Central

14 August 2017

DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications (English)

1 reference

Europe PubMed Central

14 August 2017

author name string

Cheng-Tsung Lu

1

1 reference

Europe PubMed Central

14 August 2017

Kai-Yao Huang

2

1 reference

Europe PubMed Central

14 August 2017

Min-Gang Su

3

1 reference

Europe PubMed Central

14 August 2017

Tzong-Yi Lee

4

1 reference

Europe PubMed Central

14 August 2017

Neil Arvin Bretaña

5

1 reference

Europe PubMed Central

14 August 2017

Wen-Chi Chang

6

1 reference

Europe PubMed Central

14 August 2017

Yi-Ju Chen

7

1 reference

Europe PubMed Central

14 August 2017

Yu-Ju Chen

8

1 reference

Europe PubMed Central

14 August 2017

Hsien-Da Huang

9

1 reference

Europe PubMed Central

14 August 2017

language of work or name

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publication date

27 November 2012

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Europe PubMed Central

14 August 2017

Nucleic Acids Research

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Europe PubMed Central

14 August 2017

41

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Europe PubMed Central

14 August 2017

Database issue

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Europe PubMed Central

14 August 2017

D295-305

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Europe PubMed Central

14 August 2017

copyright license

Creative Commons Attribution-NonCommercial 3.0 Unported

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

0 references

Identifying protein phosphorylation sites with kinase substrate specificity on human viruses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

dbSNO: a database of cysteine S-nitrosylation

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

PupDB: a database of pupylated proteins

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30 September 2017

Structural basis for recognition of H3K56-acetylated histone H3–H4 by the chaperone Rtt106

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30 September 2017

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

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

The Gene Ontology: enhancements for 2011

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30 September 2017

SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity

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30 September 2017

PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity

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30 September 2017

Biomolecules in the computer: Jmol to the rescue

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

dbOGAP - an integrated bioinformatics resource for protein O-GlcNAcylation.

1 reference

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30 September 2017

TMPad: an integrated structural database for helix-packing folds in transmembrane proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

PHOSIDA 2011: the posttranslational modification database

1 reference

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30 September 2017

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

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30 September 2017

RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

The RCSB Protein Data Bank: redesigned web site and web services

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

S-alkylating labeling strategy for site-specific identification of the s-nitrosoproteome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Structures of membrane proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Structural Basis for Acetylated Histone H4 Recognition by the Human BRD2 Bromodomain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

QuickGO: a web-based tool for Gene Ontology searching

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

A comprehensive resource for integrating and displaying protein post-translational modifications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Transmembrane protein topology prediction using support vector machines

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

SysPTM: a systematic resource for proteomic research on post-translational modifications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Human Protein Reference Database--2009 update

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

InterPro: the integrative protein signature database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

NetworKIN: a resource for exploring cellular phosphorylation networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

TOPDB: topology data bank of transmembrane proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

IntAct--open source resource for molecular interaction data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

MINT: the Molecular INTeraction database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

STRING 7--recent developments in the integration and prediction of protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Reading protein modifications with interaction domains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Identification of S-nitrosylation motifs by site-specific mapping of the S-nitrosocysteine proteome in human vascular smooth muscle cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

OPM: orientations of proteins in membranes database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

dbPTM: an information repository of protein post-translational modification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Human protein reference database--2006 update

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

PINT: Protein-protein Interactions Thermodynamic Database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

PDB_TM: selection and membrane localization of transmembrane proteins in 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=3531199

30 September 2017

The Universal Protein Resource (UniProt)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Annotation of post-translational modifications in the Swiss-Prot knowledge base

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

The RESID Database of Protein Modifications as a resource and annotation tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

WebLogo: A Sequence Logo Generator

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Post-translational modifications and their biological functions: proteomic analysis and systematic approaches

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

UniProt: the Universal Protein knowledgebase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

The COG database: an updated version includes eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Proteomic analysis of post-translational modifications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Molecular recognition by SH2 domains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

S-nitrosylation is emerging as a specific and fundamental posttranslational protein modification: head-to-head comparison with O-phosphorylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

The PSIPRED protein structure prediction server

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

ProTherm: Thermodynamic Database for Proteins and Mutants.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Differential effects of nitric oxide-mediated S-nitrosylation on p50 and c-jun DNA binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

The ProDom database of protein domain families

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Pfam: a comprehensive database of protein domain families based on seed alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

PRINTS--a database of protein motif fingerprints.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

Effects of site-specific amino acid modification on protein interactions and biological function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

30 September 2017

PROSITE: a dictionary of sites and patterns in proteins

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30 September 2017

(S)NO signals: translocation, regulation, and a consensus motif

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28 June 2018

Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

21 September 2018

Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

21 September 2018

N-Ace: using solvent accessibility and physicochemical properties to identify protein N-acetylation sites.

1 reference

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21 September 2018

Incorporating structural characteristics for identification of protein methylation sites

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21 September 2018

PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3531199

21 September 2018

UbiProt: a database of ubiquitylated proteins

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21 September 2018

The Phosphorylation Site Database: A guide to the serine-, threonine-, and/or tyrosine-phosphorylated proteins in prokaryotic organisms

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21 September 2018

RVP-net: online prediction of real valued accessible surface area of proteins from single sequences.

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21 September 2018

Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: structural analysis of the peptide complexes with SH2 domains.

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21 September 2018

Thermodynamic database for protein-nucleic acid interactions (ProNIT).

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21 September 2018

Differential effects of nitric oxide–mediated S-nitrosylation on p50 and c-jun DNA binding

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS1229

21 January 2018

Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites

1 reference

https://pubmed.ncbi.nlm.nih.gov/23193290

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKS1229

1 reference

Europe PubMed Central

14 August 2017

DBLP publication ID

journals/nar/LuHSLBCCCH13

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

Europe PubMed Central

14 August 2017

1 reference

Europe PubMed Central

14 August 2017

ResearchGate publication ID

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