A5049569891- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Genetics, Bioinformatics, and Biomedical Research
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Bacteriophages and microbial interactions
- Glycosylation and Glycoproteins Research
- Bacterial Genetics and Biotechnology
- Mass Spectrometry Techniques and Applications
- Enzyme Production and Characterization
- Machine Learning in Materials Science
- vaccines and immunoinformatics approaches
- Antimicrobial Peptides and Activities
- CAR-T cell therapy research
- Advanced Proteomics Techniques and Applications
- Antibiotic Resistance in Bacteria
- Biofuel production and bioconversion
- Neurobiology and Insect Physiology Research
- Hearing, Cochlea, Tinnitus, Genetics
University of Basel
2016-2025
SIB Swiss Institute of Bioinformatics
2016-2025
Stanford University
2023
Research Institute for Bioscience and Biotechnology
2023
Institute for Bioscience and Biotechnology Research
2023
Italian Institute of Technology
2012
Adam Mickiewicz University in Poznań
2011
Harvard University
2010
Lawrence Livermore National Laboratory
2008
University of Geneva
2003
Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows servers simplify streamline homology process, also allowing users without a specific computational expertise generate reliable models have easy access results, their visualization interpretation. Here, we present update SWISS-MODEL server, which pioneered field of...
Homology models of proteins are great interest for planning and analysing biological experiments when no experimental three-dimensional structures available. Building homology requires specialized programs up-to-date sequence structural databases. Integrating all required tools, databases into a single web-based workspace facilitates access to modelling from computer with web connection without the need downloading installing large program packages databases.SWISS-MODEL is integrated service...
SWISS-MODEL (http://swissmodel.expasy.org) is a server for automated comparative modeling of three-dimensional (3D) protein structures. It pioneered the field starting in 1993 and most widely-used free web-based facility today. In 2002 computed 120 000 user requests 3D models. provides several levels interaction through its World Wide Web interface: ‘first approach mode’ only an amino acid sequence submitted to build model. Template selection, alignment model building are done completely by...
Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces reliable without the need complex software packages or downloading large databases. Here, we describe latest version of expert system protein modelling. The template library provides annotation quaternary and essential ligands co-factors allow building complete...
Abstract Motivation: Quality assessment of protein structures is an important part experimental structure validation and plays a crucial role in prediction, where the predicted models may contain substantial errors. Most current scoring functions are primarily designed to rank alternative same sequence supporting model selection, whereas prediction absolute quality individual has received little attention field. However, reliable estimates assess suitability for specific biomedical...
SWISS-MODEL Repository (http://swissmodel.expasy.org/repository/) is a database of 3D protein structure models generated by the homology-modelling pipeline. The aim to provide access an up-to-date collection annotated automated homology modelling for all sequences in Swiss-Prot and relevant organisms. Regular updates ensure that target coverage complete, are built using most recent sequence template databases, improvements underlying pipeline fully utilised. As September 2008, contains 3.4...
SWISS-MODEL pioneered the field of automated modeling as first protein service on Internet. In combination with visualization tool Swiss-PdbViewer, Internet-based Workspace and Repository, it provides a fully integrated sequence to structure analysis platform. This computational environment is made freely available scientific community aim hide complexity structural bioinformatics encourage bench scientists make use ever-increasing information available. Indeed, over last decade,...
SWISS-MODEL Repository (SMR) is a database of annotated 3D protein structure models generated by the automated homology modeling pipeline. It currently holds >400 000 high quality covering almost 20% Swiss-Prot/UniProtKB entries. In this manuscript, we provide an update features and functionalities which have been implemented recently. We address improvements in target coverage, model estimates, functional annotations improved in-page visualization. also introduce new concept includes...
Abstract Motivation: The assessment of protein structure prediction techniques requires objective criteria to measure the similarity between a computational model and experimentally determined reference structure. Conventional measures based on global superposition carbon α atoms are strongly influenced by domain motions do not assess accuracy local atomic details in model. Results: Local Distance Difference Test (lDDT) is superposition-free score that evaluates distance differences all...
Model quality estimation is an essential component of protein structure prediction, since ultimately the accuracy a model determines its usefulness for specific applications. Usually, in course prediction set alternative models produced, from which subsequently most accurate has to be selected. The QMEAN server provides access two scoring functions successfully tested at eighth round community-wide blind test experiment CASP. user can choose between composite function QMEAN, derives estimate...
Methods that estimate the quality of a 3D protein structure model in absence an experimental reference are crucial to determine model's utility and potential applications. Single methods assess individual models whereas consensus require ensemble as input. In this work, we extend single composite score QMEAN employs statistical potentials mean force agreement terms by introducing consensus-based distance constraint (DisCo) score.DisCo exploits distributions from experimentally determined...
Cellular processes often depend on interactions between proteins and the formation of macromolecular complexes. The impairment such can lead to deregulation pathways resulting in disease states, it is hence crucial gain insights into nature assemblies. Detailed structural knowledge about complexes protein-protein growing, but experimentally determined three-dimensional multimeric assemblies are outnumbered by supported non-structural experimental evidence. Here, we aim fill this gap modeling...
This article is an introduction to the special issue of journal PROTEINS, dedicated tenth Critical Assessment Structure Prediction (CASP) experiment assess state art in protein structure modeling. The describes conduct experiment, categories prediction included, and outlines evaluation assessment procedures. 10 CASP experiments span almost 20 years progress field modeling, there have been enormous advances methods model accuracy that period. Notable this round first sustained improvement...
CASP (critical assessment of structure prediction) assesses the state art in modeling protein from amino acid sequence. The most recent experiment (CASP13 held 2018) saw dramatic progress without use structural templates (historically "ab initio" modeling). Progress was driven by successful application deep learning techniques to predict inter-residue distances. In turn, these results drove improvements three-dimensional accuracy: With proviso that there are an adequate number sequences...
Critical assessment of structure prediction (CASP) is a community experiment to advance methods computing three-dimensional protein from amino acid sequence. Core components are rigorous blind testing and evaluation the results by independent assessors. In most recent (CASP14), deep-learning one research group consistently delivered computed structures rivaling corresponding experimental ones in accuracy. this sense, represent solution classical protein-folding problem, at least for single...
This article reports the outcome of 12th round Critical Assessment Structure Prediction (CASP12), held in 2016. CASP is a community experiment to determine state art modeling protein structure from amino acid sequence. Participants are provided sequence information and turn provide models related information. Analysis submitted structures by independent assessors provides comprehensive picture capabilities current methods, allows progress be identified. was again an exciting CASP, with...
Second messengers control a wide range of important cellular functions in eukaryotes and prokaryotes. Here we show that cyclic di-GMP, global bacterial second messenger, promotes cell cycle progression Caulobacter crescentus by mediating the specific degradation replication initiation inhibitor CtrA. During G1-to-S-phase transition, both CtrA its cognate protease ClpXP dynamically localize to old pole, where is rapidly degraded. Sequestration pole depends on PopA, newly identified di-GMP...
The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access structural information for proteins. Both experimental structures theoretical a given protein can be searched simultaneously analyzed variability. By view on information, PMP offers the opportunity apply consistent assessment validation criteria complete set available is an open project so that new methods community...
In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering validation, modelling for biomolecular small-angle (SAS) experiments. Biomolecular SAS has since continued to grow authors have increasingly adopted the guidelines. parallel, integrative/hybrid determination structures is a rapidly growing field that expanding scope structural biology. For contribute maximally this field, it essential ensure open access...
ABSTRACT Modeling of protein structure from amino acid sequence now plays a major role in structural biology. Here we report new developments and progress the CASP11 community experiment, assessing state art modeling. Notable points include following: (1) New methods for predicting three dimensional contacts resulted few spectacular template free models this CASP, whereas based on homology to proteins with experimental continue be most accurate. (2) Refinement initial models, primarily using...
Computational methods for protein structure modelling are routinely used to complement experimental determination, thus they help address a broad spectrum of scientific questions in biomedical research. The most accurate today based on homology modelling, i.e. detecting homologue the desired target sequence that can be as template modelling. Here we present versatile open source toolbox foundation flexible and computationally efficient workflows. ProMod3 is fully scriptable software platform...
We are now entering a new era in protein sequence and structure annotation, with hundreds of millions predicted structures made available through the AlphaFold database1. These models cover nearly all proteins that known, including those challenging to annotate for function or putative biological role using standard homology-based approaches. In this study, we examine extent which database has structurally illuminated 'dark matter' natural universe at high accuracy. further describe...
Abstract Computing protein structure from amino acid sequence information has been a long‐standing grand challenge. Critical assessment of prediction (CASP) conducts community experiments aimed at advancing solutions to this and related problems. Experiments are conducted every 2 years. The 2020 experiment (CASP14) saw major progress, with the second generation deep learning methods delivering accuracy comparable for many single proteins. There is an expectation that these will have much...
Abstract Prediction categories in the Critical Assessment of Structure (CASP) experiments change with need to address specific problems structure modeling. In CASP15, four new prediction were introduced: RNA structure, ligand‐protein complexes, accuracy oligomeric structures and their interfaces, ensembles alternative conformations. This paper lists technical specifications for these describes integration CASP data management system.