PTMint database of experimentally verified PTM regulation on protein–protein interaction

Erythrocyte transglutaminase-2 combats hypoxia and chronic kidney disease by promoting oxygen delivery and carnitine homeostasis

(2022) Ping Xu et al.   Cell Metabolism

Uncovering post-translational modification-associated protein–protein interactions

(2022) Shu Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Machine learning-aided engineering of hydrolases for PET depolymerization

(2022) Hongyuan Lu et al.   NATURE

A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions

(2021) Jianwei Lin et al.   MOLECULAR CELL

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications

(2021) Zhongyan Li et al.   NUCLEIC ACIDS RESEARCH

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Development of a force field for the simulation of single-chain proteins and protein-protein complexes

(2020) Stefano Piana et al.   Journal of Chemical Theory and Computation

Dissecting intercellular signaling with mass spectrometry–based proteomics

(2020) Jonathan J. Swietlik et al.   CURRENT OPINION IN CELL BIOLOGY

The HDOCK server for integrated protein–protein docking

(2020) Yumeng Yan et al.   Nature Protocols

GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins

(2020) Chenwei Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

GPS-PBS: A Deep Learning Framework to Predict Phosphorylation Sites that Specifically Interact with Phosphoprotein-Binding Domains

(2020) Yaping Guo et al.   Cells

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

Phosphorylation promotes binding affinity of Rap-Raf complex by allosteric modulation of switch loop dynamics

(2018) Devanand T et al.   Scientific Reports

PTMD: A Database of Human Disease-associated Post-translational Modifications

(2018) Haodong Xu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

qPhos: a database of protein phosphorylation dynamics in humans

(2018) Kai Yu et al.   NUCLEIC ACIDS RESEARCH

PLMD: An updated data resource of protein lysine modifications

(2017) Haodong Xu et al.   Journal of Genetics and Genomics

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

Systematic identification of phosphorylation-mediated protein interaction switches

(2017) Matthew J. Betts et al.   PLoS Computational Biology

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Phosphorylation of KLHL3 at serine 433 impairs its interaction with the acidic motif of WNK4: a molecular dynamics study

(2016) Lingyun Wang et al.   PROTEIN SCIENCE

3Dmol.js: molecular visualization with WebGL

(2014) N. Rego et al.   BIOINFORMATICS

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

New Force Field on Modeling Intrinsically Disordered Proteins

(2014) Wei Wang et al.   Chemical Biology & Drug Design

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

(2014) Pablo Minguez et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

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

Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions

(2014) Matthew J. Betts et al.   NUCLEIC ACIDS RESEARCH

INstruct: a database of high-quality 3D structurally resolved protein interactome networks

(2013) Michael J. Meyer et al.   BIOINFORMATICS

Human DEAD Box Helicase 3 Couples I B Kinase   to Interferon Regulatory Factor 3 Activation

(2013) L. Gu et al.   MOLECULAR AND CELLULAR BIOLOGY

Systematic Functional Prioritization of Protein Posttranslational Modifications

(2012) Pedro Beltrao et al.   CELL

Quantitative Chemical Proteomics Approach To Identify Post-translational Modification-Mediated Protein–Protein Interactions

(2012) Xiang Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Casein Kinase 1  Regulates an MDMX Intramolecular Interaction To Stimulate p53 Binding

(2012) S. Wu et al.   MOLECULAR AND CELLULAR BIOLOGY

An Investigation of Hierachical Protein Recruitment to the Inhibitory Platelet Receptor, G6B-b

(2012) Carmen H. Coxon et al.   PLoS One

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

Protein Phosphatase 2A Reactivates FOXO3a through a Dynamic Interplay with 14-3-3 and AKT

(2010) Amrik Singh et al.   MOLECULAR BIOLOGY OF THE CELL

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Induced fit or conformational selection for RNA/U1A folding

(2010) F. Qin et al.   RNA

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

(2010) Javier De Las Rivas et al.   PLoS Computational Biology

Identification of Novelin VivoPhosphorylation Sites of the Human Proapoptotic Protein BAD

(2009) Lisa Polzien et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification and characterization of posttranslational modification-specific binding proteins in vivo by mammalian tethered catalysis

(2009) T. M. Spektor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

 2 integrin phosphorylation on Thr758 acts as a molecular switch to regulate 14-3-3 and filamin binding

(2008) H. Takala et al.   BLOOD

Dexras1 Interacts with FE65 to Regulate FE65-Amyloid Precursor Protein-dependent Transcription

(2008) Kwok-Fai Lau et al.   JOURNAL OF BIOLOGICAL CHEMISTRY