Robert Rentzsch

• PhD
• Consultant at Institut für Innovation und Technik (iit)

Zusammenfassung Digital Credentials sind digitale Nachweise, die in verschiedenen Kontexten erbrachte Lernleistungen und Qualifikationen erfassen. Die automatische Verifizierbarkeit solcher Nachweise bildet die Grundlage für ihren sicheren und effizienten Austausch. Dafür setzen derzeit verschiedene nationale und internationale Projekte auf die Blo...

Bacterial proteins dubbed virulence factors (VFs) are a highly diverse group of sequences, whose only obvious commonality is the very property of being, more or less directly, involved in virulence. It is therefore tempting to speculate whether their prediction, based on direct sequence similarity (seqsim) to known VFs, could be enhanced or even re...

Bacterial proteins dubbed virulence factors (VFs) are a highly diverse group of sequences, whose only obvious commonality is the very property of being, more or less directly, involved in virulence. It is therefore tempting to speculate whether their prediction, based on direct sequence similarity (seqsim) to known VFs, could be enhanced or even re...

Motivation: We expect novel pathogens to arise due to their fast-paced evolution, and new species to be discovered thanks to advances in DNA sequencing and metagenomics. Moreover, recent developments in synthetic biology raise concerns that some strains of bacteria could be modified for malicious purposes. Traditional approaches to open-view patho...

Motivation: We expect novel pathogens to arise due to their fast-paced evolution, and new species to be discovered thanks to advances in DNA sequencing and metagenomics. What is more, recent developments in synthetic biology raise concerns that some strains of bacteria could be modified for malicious purposes. Traditional approaches to open-view pa...

The reliable detection of novel bacterial pathogens from next-generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely related genomes are unavailable or missing from the reference database. Here we present the machine...

The reliable detection of novel bacterial pathogens from next generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely related genomes are unavailable or missing from reference database used. Here, we present the rando...

The reliable detection of novel bacterial pathogens from next generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely related genomes are unavailable or missing from reference database used. Here, we present the rando...

There is a growing interest in the mechanisms and the prediction of how flexible peptides bind proteins, often in a highly selective and conserved manner. While both existing small-molecule docking methods and custom protocols can be used, even short peptides make difficult targets owing to their high torsional flexibility. Any benchmarking should...

Gene3D (http://gene3d.biochem.ucl.ac.uk) is a database of protein domain structure annotations for protein sequences. Domains are predicted using a library of profile HMMs from 2738 CATH superfamilies. Gene3D assigns domain annotations to Ensembl and UniProt sequence sets including >6000 cellular genomes and >20 million unique protein sequences. Th...

Here we assessed the use of domain families for predicting the functions of whole proteins. These 'functional families' (FunFams) were derived using a protocol that combines sequence clustering with supervised cluster evaluation, relying on available high-quality Gene Ontology (GO) annotation data in the latter step. In essence, the protocol groups...

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-...

CATH version 3.5 (Class, Architecture, Topology, Homology, available at http://www.cathdb.info/) contains 173 536 domains, 2626 homologous superfamilies and 1313 fold groups. When focusing on structural genomics (SG) structures, we observe that the number of new folds for CATH v3.5 is slightly less than for previous releases, and this observation s...

Most proteins comprise several domains, segments that are clearly discernable in protein structure and sequence. Over the last two decades, it has become increasingly clear that domains are often also functional modules that can be duplicated and recombined in the course of evolution. This gives rise to novel protein functions. Traditionally, prote...

Gene3D http://gene3d.biochem.ucl.ac.uk is a comprehensive database of protein domain assignments for sequences from the major sequence databases. Domains are directly mapped from structures in the CATH database or predicted using a library of representative profile HMMs derived from CATH superfamilies. As previously described, Gene3D integrates man...

CATH version 3.3 (class, architecture, topology, homology) contains 128,688 domains, 2386 homologous superfamilies and 1233 fold groups, and reflects a major focus on classifying structural genomics (SG) structures and transmembrane proteins, both of which are likely to add structural novelty to the database and therefore increase the coverage of p...

Introduction Universal Domain Structure Families Identified in the Last Universal Common Ancestor Some Domain Families Recur More Frequently and Are Structurally Very Diverse Correlation of Structural Diversity in Superfamilies with Functional Diversity To What Extent Does Function Vary Between Homologous? How Safely Can Function Be Inherited Betwe...

GeMMA (Genome Modelling and Model Annotation) is a new approach to automatic functional subfamily classification within families and superfamilies of protein sequences. A major advantage of GeMMA is its ability to subclassify very large and diverse superfamilies with tens of thousands of members, without the need for an initial multiple sequence al...

Divergence in function of homologous proteins is based on both sequence and structural changes. Overall enzyme function has been reported to diverge earlier (50% sequence identity) than overall structure (35%). We herein study the functional conservation of enzymes and non-enzyme sequences using the protein domain families in CATH-Gene3D. Despite t...

Advances in experimental and computational methods have quietly ushered in a new era in protein function annotation. This 'age of multiplicity' is marked by the notion that only the use of multiple tools, multiple evidence and considering the multiple aspects of function can give us the broad picture that 21st century biology will need to link and...

PhD students, postdocs and even senior scientists are taking continuing-education courses to improve their scientific 'hard skills' or branch out beyond the lab. Robert Rentzsch had a look around to see what's on offer. http://www.nature.com/naturejobs/science/articles/10.1038/nj7080-122a

The possible use of illicit substances and practices such as blood doping have hung over this year's Winter Olympics in Turin. news@nature.com takes a look at what has been going on. http://www.nature.com/news/2006/060224/full/news060220-18.html

Experts warn that H5N1 could become entrenched in Europe. http://www.nature.com/news/2006/060220/full/news060220-4.html

Contest to select top universities accused of political bias. http://www.nature.com/nature/journal/v439/n7074/full/439249a.html