A5046643239- Protein Structure and Dynamics
- Enzyme Structure and Function
- Scientific Computing and Data Management
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Machine Learning in Materials Science
- RNA and protein synthesis mechanisms
- Data Visualization and Analytics
- Cell Image Analysis Techniques
- Microbial Metabolic Engineering and Bioproduction
- Mass Spectrometry Techniques and Applications
- Genetics, Bioinformatics, and Biomedical Research
- Computer Graphics and Visualization Techniques
- Advanced Data Storage Technologies
- Machine Learning in Bioinformatics
- Advanced Electron Microscopy Techniques and Applications
- Simulation Techniques and Applications
- Microfluidic and Capillary Electrophoresis Applications
- Electrowetting and Microfluidic Technologies
- Escherichia coli research studies
- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- Virus-based gene therapy research
- Model-Driven Software Engineering Techniques
- Electrostatic Discharge in Electronics
Utrecht University
2012-2024
Fluigent (France)
2021
Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur
2013-2016
Université Paris-Sud
2016
Centre National de la Recherche Scientifique
2011-2015
International Life Sciences Institute Europe
2014
Institut Pasteur
2011
The prediction of the quaternary structure biomolecular macromolecules is paramount importance for fundamental understanding cellular processes and drug design. In era integrative structural biology, one way increasing accuracy modeling methods used to predict complexes include as much experimental or predictive information possible in process. This has been at core our information-driven docking approach HADDOCK. We present here updated version 2.2 HADDOCK portal, which offers new features...
Abstract Summary Recently we published PROtein binDIng enerGY (PRODIGY), a web-server for the prediction of binding affinity in protein–protein complexes. By using combination simple structural properties, such as residue-contacts made at interface, PRODIGY has demonstrated top performance compared with other state-of-the-art predictors literature. Here present an extension it, named PRODIGY-LIG, aimed protein-small ligand The predictive method, properly readapted small by making use atomic...
Protein-peptide interactions are vital for the cell. They mediate, inhibit or serve as structural components in nearly 40% of all macromolecular interactions, and often associated with diseases, making them interesting leads protein drug design. In recent years, large-scale technologies have enabled exhaustive studies on peptide recognition preferences a number peptide-binding domain families. Yet, paucity data regarding their molecular binding mechanisms together inherent flexibility makes...
Regulated deaggregation allows meningitis-causing bacteria to propagate new host cells and migrate across epithelia.
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Abstract Inaccuracies in computational molecular modeling methods are often counterweighed by brute‐force generation of a plethora putative solutions. These then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) atomic positions. Albeit widely used, these suffer from several theoretical and technical limitations (e.g., choice regions for fitting) that impair their application multicomponent systems ( N > 2), large‐scale...
We present the performance of HADDOCK, our information-driven docking software, in second edition D3R Grand Challenge. In this blind experiment, participants were requested to predict structures and binding affinities complexes between Farnesoid X nuclear receptor 102 different ligands. The models obtained Stage1 with HADDOCK ligand-specific protocol show an average ligand RMSD 5.1 Å from crystal structure. Only 6/35 targets within 2.5 reference, which prompted us investigate limiting...
We present the results for CAPRI Round 46, third joint CASP-CAPRI protein assembly prediction challenge. The comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight homo-oligomer one heterodimer proteins that could be readily modeled using templates from Protein Data Bank, often available full assembly. remaining 11 5 homodimers, 3 heterodimers, two higher-order assemblies. These were more difficult to model, as their mainly involved "ab-initio" docking...
We present SpotOn, a web server to identify and classify interfacial residues as Hot-Spots (HS) Null-Spots (NS). SpotON implements robust algorithm with demonstrated accuracy of 0.95 sensitivity 0.98 on an independent test set. The predictor was developed using ensemble machine learning approach up-sampling the minor class. It trained 53 complexes various features, based both protein 3D structure sequence. SpotOn interface is freely available at: http://milou.science.uu.nl/services/SPOTON/ .
Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state predictive methodology. Here we describe a community-wide assessment methods to predict effects mutations on protein-protein interactions. Twenty-two groups predicted comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful...
Information-driven docking is currently one of the most successful approaches to obtain structural models protein interactions as demonstrated in latest round CAPRI. While various experimental and computational techniques can be used retrieve information about binding mode, availability three-dimensional structures interacting partners remains a limiting factor. Fortunately, wealth gathered by large-scale initiatives allows for homology-based modeling significant fraction universe. Defining...
Structure determination of complex molecular machines requires a combination an increasing number experimental methods with highly specialized software geared toward each data source to properly handle the gathered data. Recently, we introduced two packages PowerFit and DisVis. These combine high-resolution structures atomic subunits density maps from cryo-electron microscopy or distance restraints, typically acquired by chemical cross-linking coupled mass spectrometry, respectively. Here,...
ABSTRACT Our information‐driven docking approach HADDOCK is a consistent top predictor and scorer since the start of its participation in CAPRI community‐wide experiment. This sustained performance due, part, to ability integrate experimental data and/or bioinformatics information into modelling process, also overall robustness scoring function used assess rank predictions. In CASP‐CAPRI Round 1 experiment we successfully selected acceptable/medium quality models for 18/14 25 targets –...
Given the need for modern researchers to produce open, reproducible scientific output, lack of standards and best practices sharing data workflows used analyze molecular dynamics (MD) simulations has become an important issue in field. There are now multiple well-established packages perform simulations, often highly tuned exploiting specific classes hardware, each with strong communities surrounding them, but very limited interoperability/transferability options. Thus, choice software...
Abstract The advances made in recent years the field of structural biology significantly increased throughput and complexity data that scientists have to deal with. Combining analyzing such heterogeneous amounts became a crucial time consumer daily tasks scientists. However, only few efforts been offer an alternative standard compartmentalized tools they use explore their involve regular back forth between them. We propose here integrated pipeline especially designed for immersive...
De novo macrocyclic peptides, derived using selection technologies such as phage and mRNA display, present unique unexpected solutions to challenging biological problems. This is due in part their unusual folds, which are able side chains ways not available canonical structures α-helices β-sheets. Despite much recent interest these molecules, folding binding behavior remains poorly characterized. In this work, we cocrystallization, docking, solution NMR of three de peptides that all bind...
Abstract The Protein Data Bank (PDB) file format remains a popular used and supported by many software to represent coordinates of macromolecular structures. It however suffers from drawbacks such as error‐prone manual editing. Because that, various toolkits have been developed facilitate its editing manipulation, but, date, there is no online tool available for this purpose. Here we present PDB‐Tools Web, flexible service manipulating PDB files. offers rich user‐friendly graphical user...
Bringing together, in a unique immersive environment, visualization and analysis of scientific complex data requires thorough approach order to fulfill scientists' specific expectations. Such an needs consider the highly heterogeneous nature data, dynamic interactions between experts large amount involved studies. Whereas small static datasets can quickly be deciphered thanks standard tools such as 3D software packages, bigger exceed analytical capacity these tools, requiring efficient...
The amount of data generated by molecular dynamics simulations large assemblies and the sheer size complexity systems studied call for new ways to analyse, steer interact with such calculations. Traditionally, analysis is performed off-line once huge simulation results have been saved disks, thereby stressing supercomputer I/O systems, making it increasingly difficult handle post-processing from scientist's office. ExaViz framework an alternative approach developed couple tools process as...
Abstract Our information‐driven docking approach HADDOCK has demonstrated a sustained performance since the start of its participation to CAPRI. This is due, in part, ability integrate data into modeling process, and robustness scoring function. We participated CAPRI both as server manual predictors. In rounds 38‐45, we have used various strategies depending on available information. These ranged from imposing restraints few residues identified literature being important for interaction,...
The pdb-tools are a collection of Python scripts for working with molecular structure data in the PDB format. They allow users to edit, convert, and validate files, from command-line, simple but efficient manner. implemented Python, without any external dependencies, freely available under open-source Apache License at https://github.com/haddocking/pdb-tools/ on PyPI (https://pypi.org/project/pdb-tools/).