Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad

The ABBA Motif Binds APC/C Activators and Is Shared by APC/C Substrates and Regulators

(2015) Barbara Di Fiore et al.   DEVELOPMENTAL CELL

xiNET: Cross-link Network Maps With Residue Resolution

(2015) Colin W. Combe et al.   MOLECULAR & CELLULAR PROTEOMICS

BioID-based Identification of Skp Cullin F-box (SCF)β-TrCP1/2E3 Ligase Substrates

(2015) Etienne Coyaud et al.   MOLECULAR & CELLULAR PROTEOMICS

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

The BioMart community portal: an innovative alternative to large, centralized data repositories

(2015) Damian Smedley et al.   NUCLEIC ACIDS RESEARCH

The EMBL-EBI bioinformatics web and programmatic tools framework

(2015) Weizhong Li et al.   NUCLEIC ACIDS RESEARCH

Gene dosage imbalances: action, reaction, and models

(2015) Reiner A. Veitia et al.   TRENDS IN BIOCHEMICAL SCIENCES

Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation

(2014) Kim Van Roey et al.   CHEMICAL REVIEWS

Insights into the anaphase-promoting complex: a molecular machine that regulates mitosis

(2014) Leifu Chang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The exosome‐binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase

(2014) Benjamin Schuch et al.   EMBO JOURNAL

Structural analysis of the KANSL1/WDR5/KANSL2 complex reveals that WDR5 is required for efficient assembly and chromatin targeting of the NSL complex

(2014) J. Dias et al.   GENES & DEVELOPMENT

A Chromosome-Centric Analysis of Antibodies Directed toward the Human Proteome Using Antibodypedia

(2014) Tove Alm et al.   JOURNAL OF PROTEOME RESEARCH

A Million Peptide Motifs for the Molecular Biologist

(2014) Peter Tompa et al.   MOLECULAR CELL

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis

(2014) Daniel V. Veres et al.   NUCLEIC ACIDS RESEARCH

MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins

(2014) Emilio Potenza et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Dimerization-induced allostery in protein kinase regulation

(2014) Hugo Lavoie et al.   TRENDS IN BIOCHEMICAL SCIENCES

Signalosome assembly by domains undergoing dynamic head-to-tail polymerization

(2014) Mariann Bienz   TRENDS IN BIOCHEMICAL SCIENCES

COMPARTMENTS: unification and visualization of protein subcellular localization evidence

(2014) J. X. Binder et al.   Database-The Journal of Biological Databases and Curation

The transience of transient overexpression

(2013) Toby J Gibson et al.   NATURE METHODS

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

Analysis Tool Web Services from the EMBL-EBI

(2013) Hamish McWilliam et al.   NUCLEIC ACIDS RESEARCH

The eukaryotic linear motif resource ELM: 10 years and counting

(2013) Holger Dinkel et al.   NUCLEIC ACIDS RESEARCH

TreeFam v9: a new website, more species and orthology-on-the-fly

(2013) Fabian Schreiber et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

From proteomes to complexomes in the era of systems biology

(2013) Trevor Clancy et al.   PROTEOMICS

The switches.ELM Resource: A Compendium of Conditional Regulatory Interaction Interfaces

(2013) K. Van Roey et al.   Science Signaling

Ras and extracellular signal-regulated kinase signaling in thymocytes and T cells

(2013) Robert L. Kortum et al.   TRENDS IN IMMUNOLOGY

MisPred: a resource for identification of erroneous protein sequences in public databases

(2013) Alinda Nagy et al.   Database-The Journal of Biological Databases and Curation

Wnt/β-Catenin Signaling and Disease

(2012) Hans Clevers et al.   CELL

Motif switches: decision-making in cell regulation

(2012) Kim Van Roey et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Interactions via intrinsically disordered regions: What kind of motifs?

(2012) Rita Pancsa et al.   IUBMB LIFE

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

Sequence and structural analyses of nuclear export signals in the NESdb database

(2012) Darui Xu et al.   MOLECULAR BIOLOGY OF THE CELL

Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

(2012) Jonathan D. Ellis et al.   MOLECULAR CELL

Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks

(2012) Marija Buljan et al.   MOLECULAR CELL

iELM--a web server to explore short linear motif-mediated interactions

(2012) R. J. Weatheritt et al.   NUCLEIC ACIDS RESEARCH

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

(2012) Norman E. Davey et al.   NUCLEIC ACIDS RESEARCH

PepSite: prediction of peptide-binding sites from protein surfaces

(2012) L. G. Trabuco et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

D2P2: database of disordered protein predictions

(2012) Matt E. Oates et al.   NUCLEIC ACIDS RESEARCH

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

(2012) F. Herzog et al.   SCIENCE

Linear motifs: lost in (pre)translation

(2012) Robert J. Weatheritt et al.   TRENDS IN BIOCHEMICAL SCIENCES

Correction: A Dynamic View of Domain-Motif Interactions

(2012) Eyal Akiva et al.   PLoS Computational Biology

A Smad action turnover switch operated by WW domain readers of a phosphoserine code

(2011) E. Aragon et al.   GENES & DEVELOPMENT

Cytosolic aggregates perturb the degradation of nontranslocated secretory and membrane proteins

(2011) Oishee Chakrabarti et al.   MOLECULAR BIOLOGY OF THE CELL

Attributes of short linear motifs

(2011) Norman E. Davey et al.   Molecular BioSystems

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

SLiMSearch 2.0: biological context for short linear motifs in proteins

(2011) N. E. Davey et al.   NUCLEIC ACIDS RESEARCH

Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information

(2011) M. C. Good et al.   SCIENCE

RNA–protein interactions in human health and disease

(2011) Ahmad M. Khalil et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Exploring the spatial and temporal organization of a cell’s proteome

(2010) Martin Beck et al.   JOURNAL OF STRUCTURAL BIOLOGY

Decoding signalling networks by mass spectrometry-based proteomics

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

SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs

(2010) N. E. Davey et al.   NUCLEIC ACIDS RESEARCH

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

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

LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana

(2010) Shruti Rastogi et al.   NUCLEIC ACIDS RESEARCH

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

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

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

The LAT Story: A Tale of Cooperativity, Coordination, and Choreography

(2010) L. Balagopalan et al.   Cold Spring Harbor Perspectives in Biology

Fragilities Caused by Dosage Imbalance in Regulation of the Budding Yeast Cell Cycle

(2010) Kazunari Kaizu et al.   PLoS Genetics

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

Cell Signaling in Space and Time: Where Proteins Come Together and When They're Apart

(2009) J. D. Scott et al.   SCIENCE

Cell regulation: determined to signal discrete cooperation

(2009) Toby J. Gibson   TRENDS IN BIOCHEMICAL SCIENCES

Robustness: mechanisms and consequences

(2009) Joanna Masel et al.   TRENDS IN GENETICS

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences

(2008) Claudia Chica et al.   BMC BIOINFORMATICS

Understanding eukaryotic linear motifs and their role in cell signaling and regulation

(2008) Francesca Diella   Frontiers in Bioscience-Landmark

The Human Protein Atlas-a tool for pathology

(2008) F Pontén et al.   JOURNAL OF PATHOLOGY

Antibodypedia, a Portal for Sharing Antibody and Antigen Validation Data

(2008) Erik Björling et al.   MOLECULAR & CELLULAR PROTEOMICS

PiSite: a database of protein interaction sites using multiple binding states in the PDB

(2008) M. Higurashi et al.   NUCLEIC ACIDS RESEARCH

Minimotif miner 2nd release: a database and web system for motif search

(2008) S. Rajasekaran et al.   NUCLEIC ACIDS RESEARCH