A5070513438- Drug-Induced Hepatotoxicity and Protection
- Vitamin C and Antioxidants Research
- Metabolomics and Mass Spectrometry Studies
- Liver Disease Diagnosis and Treatment
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Enzyme Structure and Function
- Genetics, Bioinformatics, and Biomedical Research
- Escherichia coli research studies
- Microtubule and mitosis dynamics
- Computational Drug Discovery Methods
- RNA Research and Splicing
- Fractal and DNA sequence analysis
- Cellular transport and secretion
- Cell Image Analysis Techniques
- Peer-to-Peer Network Technologies
- COVID-19 diagnosis using AI
- Advanced Proteomics Techniques and Applications
- Scientific Computing and Data Management
- Cancer Research and Treatment
- Microbial Metabolic Engineering and Bioproduction
Weihenstephan-Triesdorf University of Applied Sciences
2020-2023
Technical University of Munich
2014-2022
Garvan Institute of Medical Research
2021
European Molecular Biology Laboratory
2010
Philipps University of Marburg
2000-2001
PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with protein it returns: multiple alignments, predicted aspects structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) strands, coiled-coil regions, disulfide bonds disordered regions) function. The service incorporates methods the identification regions (ConSurf), homology-based inference Gene Ontology terms...
Abstract Since 1992 PredictProtein (https://predictprotein.org) is a one-stop online resource for protein sequence analysis with its main site hosted at the Luxembourg Centre Systems Biomedicine (LCSB) and queried monthly by over 3,000 users in 2020. was first Internet server predictions. It pioneered combining evolutionary information machine learning. Given as input, outputs multiple alignments, predictions of structure 1D 2D (secondary structure, solvent accessibility, transmembrane...
Significance A key remaining frontier in our understanding of biological systems is the “dark proteome”—that is, regions proteins where molecular conformation completely unknown. We systematically surveyed these regions, finding that nearly half proteome eukaryotes dark and that, surprisingly, most darkness cannot be accounted for. also found has unexpected features, including an association with secretory tissues, disulfide bonding, low evolutionary conservation, very few known interactions...
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora databases tools deployed, technically complex diverse implementations, across spectrum disciplines. The corpus documentation resources is fragmented Web, with much redundancy, has lacked common standard information. outcome scientists must often struggle find, understand, compare use best for...
Article14 September 2021Open Access Transparent process SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms Seán I O'Donoghue Corresponding Author [email protected] orcid.org/0000-0001-9520-6623 Garvan Institute of Medical Research, Darlinghurst, NSW, Australia CSIRO Data61, Canberra, ACT, School Biotechnology Biomolecular Sciences (UNSW), Kensington, Search for more papers by this author Andrea Schafferhans orcid.org/0000-0002-5569-6186...
Genomes of E. coli, including that the human pathogen Escherichia coli O157:H7 (EHEC) EDL933, still harbor undetected protein-coding genes which, apparently, have escaped annotation due to their small size and non-essential function. To find such genes, global gene expression EHEC EDL933 was examined, using strand-specific RNAseq (transcriptome), ribosomal footprinting (translatome) mass spectrometry (proteome). Using above methods, 72 short, non-annotated were detected. All these showed...
In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition transcriptome, translatome (RIBOseq) enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature high osmotic pressure. All...
Abstract Since 1992 PredictProtein ( https://predictprotein.org ) is a one-stop online resource for protein sequence analysis with its main site hosted at the Luxembourg Centre Systems Biomedicine (LCSB) and queried monthly by over 3,000 users in 2020. was first Internet server predictions. It pioneered combining evolutionary information machine learning. Given as input, outputs multiple alignments, predictions of structure 1D 2D (secondary structure, solvent accessibility, transmembrane...
Abstract Summary: In this paper we present SRS 3D, a new service that allows users to easily and rapidly find all related structures for given target sequence; can then be viewed together with sequences, alignments sequence features (currently from UniProt, InterPro PDB). Extensive user feedback confirms 3D is intuitive useful especially those not expert in structures. Availability: An server provided at http://srs3d.ebi.ac.uk/ Supplementary information: Complete documentation available...
Abstract In response to the COVID-19 pandemic, many life scientists are focused on SARS-CoV-2. To help them use available structural data, we systematically modeled all viral proteins using related 3D structures, generating 872 models that provide detail not elsewhere. organise these models, created a coverage map: novel, one-stop visualization summarizing what is — and known about structure of proteome. The map highlights evidence for protein interactions, mimicry, hijacking; it also helps...
Abstract Despite substantial and successful projects for structural genomics, many proteins remain which neither experimental structures nor homology‐based models are known any part of the amino acid sequence. These have been called "dark proteins," in contrast to non‐dark proteins, at least sequence has a or inferred structure. It hypothesized that may be more abundantly expressed than dark much fewer relatives. Surprisingly, opposite observed: human had quite similar levels expression,...
To understand the molecular mechanisms that give rise to a protein's function, biologists often need (i) find and access all related atomic-resolution 3D structures, (ii) map sequence-based features (e.g., domains, single-nucleotide polymorphisms, post-translational modifications) onto these structures. streamline processes we recently developed Aquaria, resource offering unprecedented protein structure information based on an all-against-all comparison of SwissProt PDB sequences. In this...
We introduce the PSSH ('Protein Sequence-to-Structure Homologies') database derived from HSSP2, an improved version of HSSP ('Homology-derived Secondary Structure Proteins') [Dodge et al. (1998) Nucleic Acids Res. , 26, 313–315]. Whereas each entry lists all protein sequences related to a given 3D structure, is 'inverse', with listing structures sequence. In addition, we two other databases: HSSPchain, in which PDB chain, and HSSPalign, gives details one sequence aligned onto chain. This...
The (neuro)hormones gastrin and cholecystokinin (CCK) share a common C-terminal tetrapeptide amide sequence that has been recognized as the message portion while N-terminal extensions are responsible for CCKA CCKB receptor subtype selectivity avidity. 1,4-Benzodiazepine derivatives potent selective antagonists of these receptors, according to comparative molecular field analysis, structures nonpeptidic compounds could well mimic peptide agonists at least in terms spatial array aromatic...
Abstract Motivation Variant analysis is a core task in bioinformatics that requires integrating data from many sources. This process can be helped by using 3D structures of proteins, which provide spatial context insight into how variants affect function. Many available tools help with mapping onto structures; but each has specific restrictions, the result researchers fail to benefit valuable insights could gained structural data. Results To address this, we have created streamlined system...