A5004328524- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Protein Structure and Dynamics
- Ubiquitin and proteasome pathways
- Bioinformatics and Genomic Networks
- Microtubule and mitosis dynamics
- Machine Learning in Bioinformatics
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Genetic and Kidney Cyst Diseases
- Protist diversity and phylogeny
- Glycosylation and Glycoproteins Research
- Bacteriophages and microbial interactions
- Advanced Proteomics Techniques and Applications
- Genetics and Neurodevelopmental Disorders
- Enzyme Structure and Function
- Monoclonal and Polyclonal Antibodies Research
- Bacterial Genetics and Biotechnology
- Cellular transport and secretion
- Fungal and yeast genetics research
- Genetic Neurodegenerative Diseases
- Protein Kinase Regulation and GTPase Signaling
- Mitochondrial Function and Pathology
- 14-3-3 protein interactions
European Molecular Biology Laboratory
2015-2024
European Molecular Biology Laboratory
2007-2024
Los Alamos National Laboratory
2023
Max Planck Society
2019
Max Planck Institute for Biological Cybernetics
2019
Heidelberg University
2015
European Bioinformatics Institute
1997-2013
Centre National de la Recherche Scientifique
2011-2013
Wellcome Trust
2013
Université Claude Bernard Lyon 1
2013
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for divergent protein sequences. Firstly, individual weights are assigned to each in a partial order downweight near-duplicate sequences and up-weight most ones. Secondly, amino acid substitution matrices varied at different stages according divergence be aligned. Thirdly, residue-specific gap penalties locally reduced hydrophilic regions encourage new gaps potential loop rather than...
CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program W. The system easy to use, providing an integrated performing and profile alignments analysing results. displays in window on screen. A versatile colouring scheme allows user highlight conserved features alignment. Pull-down menus provide all options required traditional New include: ability cut-and-paste sequences change order of alignment, selection subset be realigned, sub-range...
Abstract Summary: The Clustal W and X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of algorithms future has allowed proper porting to latest versions Linux, Macintosh Windows operating systems. Availability: can be run on-line from EBI web server: http://www.ebi.ac.uk/tools/clustalw2. source code executables for Windows, Linux computers are available ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/ Contact:...
The Clustal programs are widely used for carrying out automatic multiple alignment of nucleotide or amino acid sequences. most familiar version is ClustalW, which uses a simple text menu system that portable to more less all computer systems. ClustalX features graphical user interface and some powerful utilities aiding the interpretation alignments preferred interactive usage. Users may run remotely from several sites using Web be downloaded locally on PCs, Macintosh, Unix computers....
Two methods for increasing the length of DNA sequence data that can be read off a polyacrylamide gel are described. We have developed rapid way to pour buffer concentration gradient that, by altering vertical band separation on an autoradiograph, allows more obtained from gel. also show use deoxyadenosine 5'-(alpha-[35S]thio)triphosphate as label incorporated in dideoxynucleotide reactions increases sharpness bands autoradiograph and so resolution achieved.
Ionotropic glutamate receptors (iGluRs) are a highly conserved family of ligand-gated ion channels present in animals, plants, and bacteria, which best characterized for their roles synaptic communication vertebrate nervous systems. A variant subfamily iGluRs, the Receptors (IRs), was recently identified as new class olfactory fruit fly, Drosophila melanogaster, hinting at broader function this channel detection environmental, well intercellular, chemical signals. Here, we investigate origin...
The Phospho.ELM resource ( http://phospho.elm.eu.org ) is a relational database designed to store in vivo and vitro phosphorylation data extracted from the scientific literature phosphoproteomic analyses. has been actively developed for more than 7 years currently comprises 42 574 serine, threonine tyrosine non-redundant sites. Several new features have implemented, such as structural disorder/order accessibility information conservation score. Additionally, of phosphosites can now be...
Traditionally, protein-protein interactions were thought to be mediated by large, structured domains. However, it has become clear that the interactome comprises a wide range of binding interfaces with varying degrees flexibility, ranging from rigid globular domains disordered regions natively lack structure. Enrichment for disorder in highly connected hub proteins and its correlation organism complexity hint at functional importance regions. Nevertheless, they have not yet been extensively...
Linear motifs are short, evolutionarily plastic components of regulatory proteins and provide low-affinity interaction interfaces. These compact modules play central roles in mediating every aspect the functionality cell. They particularly prominent cell signaling, controlling protein turnover directing localization. Given their importance, our understanding is surprisingly limited, largely as a result difficulty discovery, both experimentally computationally. The Eukaryotic Motif (ELM)...
Many aspects of cell signalling, trafficking, and targeting are governed by interactions between globular protein domains short peptide segments. These often bind multiple peptides that share a common sequence pattern, or "linear motif" (e.g., SH3 binding to PxxP). known, though comparatively few linear motifs have been discovered. Their length (three eight residues), the fact they reside in disordered regions proteins makes them difficult detect through comparison experiment. Nevertheless,...
The Eukaryotic Linear Motif (ELM) resource (http://elm.eu.org) is a manually curated database of short linear motifs (SLiMs). In this update, we present the latest additions to resource, along with more improvements web interface. ELM 2016 contains than 240 different motif classes over 2700 experimentally validated instances, from 2400 scientific publications. addition, data have been made available as individually searchable pages and are downloadable in various formats.
The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short motifs (SLiMs). For >10 years, this has provided the scientific community with freely accessible guide to biology function of motifs. current version ELM contains ∼200 different classes over 2400 experimentally validated instances manually curated from >2000 publications. Furthermore, detailed motif-mediated interactions been annotated made available in...
Abstract The eukaryotic linear motif (ELM) resource is a repository of manually curated experimentally validated short motifs (SLiMs). Since the initial release almost 20 years ago, ELM has become an indispensable for molecular biology community investigating functional regions in many proteins. In this update, we have added 21 novel classes, made major revisions to 12 classes and >400 new instances mostly focused on DNA damage, cytoskeleton, SH2-binding phosphotyrosine mimicry by...
A resource centered on short linear motifs provides a repository and exploratory tool for conditional protein interactions.