dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins

Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities

(2015) Van-Nui Nguyen et al.   BMC BIOINFORMATICS

GSHSite: Exploiting an Iteratively Statistical Method to Identify S-Glutathionylation Sites with Substrate Specificity

(2015) Yi-Ju Chen et al.   PLoS One

Reactive Oxygen Species-Responsive Protein Modification and Its Intracellular Delivery for Targeted Cancer Therapy

(2014) Ming Wang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

dbGSH: a database of S-glutathionylation

(2014) Yi-Ju Chen et al.   BIOINFORMATICS

Characterization and identification of protein O-GlcNAcylation sites with substrate specificity

(2014) Hsin-Yi Wu et al.   BMC BIOINFORMATICS

Decoding the S-Nitrosoproteomic Atlas in Individualized Human Colorectal Cancer Tissues Using a Label-Free Quantitation Strategy

(2014) Yi-Ju Chen et al.   JOURNAL OF PROTEOME RESEARCH

dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation

(2014) Yi-Ju Chen et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Survey of phosphorylation near drug binding sites in the Protein Data Bank (PDB) and their effects

(2014) Kyle P. Smith et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

RegPhos 2.0: an updated resource to explore protein kinase–substrate phosphorylation networks in mammals

(2014) Kai-Yao Huang et al.   Database-The Journal of Biological Databases and Curation

An Intelligent System for Identifying Acetylated Lysine on Histones and Nonhistone Proteins

(2014) Cheng-Tsung Lu et al.   Biomed Research International

Parkin Induces Upregulation of 40S Ribosomal Protein SA and Posttranslational Modification of Cytokeratins 8 and 18 in Human Cervical Cancer Cells

(2013) Dae-Geun Song et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures

(2013) Min-Gang Su et al.   BMC BIOINFORMATICS

ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins

(2013) Kai-Yao Huang et al.   BMC BIOINFORMATICS

Mineralocorticoid Receptor Phosphorylation Regulates Ligand Binding and Renal Response to Volume Depletion and Hyperkalemia

(2013) Shigeru Shibata et al.   Cell Metabolism

topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins

(2013) Min-Gang Su et al.   NUCLEIC ACIDS RESEARCH

CPLM: a database of protein lysine modifications

(2013) Zexian Liu et al.   NUCLEIC ACIDS RESEARCH

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

In silico Platform for Prediction of N-, O- and C-Glycosites in Eukaryotic Protein Sequences

(2013) Jagat Singh Chauhan et al.   PLoS One

dbSNO: a database of cysteine S-nitrosylation

(2012) Tzong-Yi Lee et al.   BIOINFORMATICS

PupDB: a database of pupylated proteins

(2012) Chun-Wei Tung   BMC BIOINFORMATICS

Protein S-nitrosylation and cancer

(2012) Zhaoqing Wang   CANCER LETTERS

PhosPhAt goes kinases—searchable protein kinase target information in the plant phosphorylation site database PhosPhAt

(2012) Monika Zulawski et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Cheng-Tsung Lu et al.   NUCLEIC ACIDS RESEARCH

Identifying Protein Phosphorylation Sites with Kinase Substrate Specificity on Human Viruses

(2012) Neil Arvin Bretaña et al.   PLoS One

Accurate Prediction of Protein Catalytic Residues by Side Chain Orientation and Residue Contact Density

(2012) Yu-Tung Chien et al.   PLoS One

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

(2011) Tzong-Yi Lee et al.   BMC BIOINFORMATICS

dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation

(2011) Jinlian Wang et al.   BMC BIOINFORMATICS

E3Net: A System for Exploring E3-mediated Regulatory Networks of Cellular Functions

(2011) Youngwoong Han et al.   MOLECULAR & CELLULAR PROTEOMICS

Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis

(2011) Renu Goel et al.   Molecular BioSystems

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

SNOSite: Exploiting Maximal Dependence Decomposition to Identify Cysteine S-Nitrosylation with Substrate Site Specificity

(2011) Tzong-Yi Lee et al.   PLoS One

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

(2010) Shu-An Chen et al.   BMC BIOINFORMATICS

Ubiquitylation and SUMOylation of Cardiac Ion Channels

(2010) Jean-Sébastien Rougier et al.   JOURNAL OF CARDIOVASCULAR PHARMACOLOGY

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

(2010) Tzong-Yi Lee et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Novel Approach for Untargeted Post-translational Modification Identification Using Integer Linear Optimization and Tandem Mass Spectrometry

(2010) Richard C. Baliban et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Tzong-Yi Lee et al.   NUCLEIC ACIDS RESEARCH

Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

(2009) Pawel Durek et al.   BMC BIOINFORMATICS

O-GlcNAc Protein Modification in Cancer Cells Increases in Response to Glucose Deprivation through Glycogen Degradation

(2009) Jeong Gu Kang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Incorporating structural characteristics for identification of protein methylation sites

(2009) Dray-Ming Shien et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural Analysis of Cysteine S-Nitrosylation: A Modified Acid-Based Motif and the Emerging Role of Trans-Nitrosylation

(2009) Stefano M. Marino et al.   JOURNAL OF MOLECULAR BIOLOGY

SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications

(2009) Hong Li et al.   MOLECULAR & CELLULAR PROTEOMICS

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH