A5050454940- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Advanced Proteomics Techniques and Applications
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Metabolomics and Mass Spectrometry Studies
- Bacterial Genetics and Biotechnology
- Molecular spectroscopy and chirality
- Glycosylation and Glycoproteins Research
- Mass Spectrometry Techniques and Applications
- Computational Drug Discovery Methods
- RNA Research and Splicing
- Monoclonal and Polyclonal Antibodies Research
- Biochemical and Structural Characterization
- Bacteriophages and microbial interactions
- Scientific Computing and Data Management
- Microbial Metabolic Engineering and Bioproduction
- RNA modifications and cancer
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Rare Diseases
- HIV Research and Treatment
- Analytical Chemistry and Chromatography
- CRISPR and Genetic Engineering
Vrije Universiteit Brussel
2015-2024
Université Libre de Bruxelles
2002-2024
VIB-VUB Center for Structural Biology
2015-2024
Institute of Bioinformatics
2019-2024
Victoria University of Bangladesh
2018-2023
Vlaams Instituut voor Biotechnologie
2013-2020
Centre for Structural Systems Biology
2019
European Bioinformatics Institute
2005-2014
Wellcome Trust
2002-2012
University of Wisconsin–Madison
2011
Abstract To address data management and exchange problems in the nuclear magnetic resonance (NMR) community, Collaborative Computing Project for NMR community (CCPN) created a “Data Model” that describes all different types of information needed an structural study, from molecular structure parameters to coordinates. This paper development set software applications use Data Model its associated libraries, thus validating approach. These are freely available provide pipeline high‐throughput...
Abstract Background ACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies generation of small molecule topologies and parameters for variety molecular dynamics programmes like GROMACS, CHARMM CNS. It written in Python programming language was developed as tool interfacing with other based applications such CCPN suite (for NMR data analysis) ARIA structure calculations from data). open source code, under GNU GPL v3, available...
One of the major open challenges in structural biology is to achieve effective descriptions disordered states proteins. This problem difficult because these are conformationally highly heterogeneous and cannot be represented as single structures, therefore it necessary characterize their conformational properties terms probability distributions. Here we show that possible obtain quantitative information about particularly important types distributions, populations secondary structure...
Abstract State‐of‐the‐art methods based on CNS and CYANA were used to recalculate the nuclear magnetic resonance (NMR) solution structures of 500+ proteins for which coordinates NMR restraints are available from Protein Data Bank. Curated obtained BioMagResBank FRED database. Although original determined by various methods, they all recalculated refined subsequently restrained molecular dynamics (CNS) in a hydrated environment. We present an extensive analysis results, terms quality...
The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide partners to enhance the quality and consistency of international archive bio-macromolecular structure data, (PDB). PDBe also works closely collaborators at European Bioinformatics Institute scientific community around world databases services by adding curated maintained derived data existing structural PDB. We have developed a new database infrastructure based on remediated PDB...
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. current release holds information on more than 800 entries IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist function without a well-defined three-dimensional structure. We have re-curated previous to purge DisProt from conflicting cases, also the functional classification scheme reflect continuous advance field past 10 years...
Intrinsically disordered proteins, defying the traditional protein structure-function paradigm, are a challenge to study experimentally. Because large part of our knowledge rests on computational predictions, it is crucial that their accuracy high. The Critical Assessment Intrinsic Disorder prediction (CAID) experiment was established as community-based blind test determine state art in intrinsically regions and subset residues involved binding. A total 43 methods were evaluated dataset 646...
Abstract The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including doubling protein entries, a new disorder ontology, improvements annotation format and completely website. website includes redesigned graphical interface, better search engine, clearer API for programmatic access interface that integrates text mining...
Abstract The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in version 4, regarding the format, with novel types of an improved update process. new website includes a re-designed user interface, more effective search engine advanced API programmatic access. schema gives flexibility users, as well simplifying maintenance updates. In addition, entry page visualisation tools...
The MobiDB (URL: mobidb.bio.unipd.it) database of protein disorder and mobility annotations has been significantly updated upgraded since its last major renewal in 2014. Several curated datasets for intrinsic folding upon binding have integrated from specialized databases. indirect evidence also expanded to better capture information available the PDB, such as high temperature residues X-ray structures overall conformational diversity. Novel nuclear magnetic resonance chemical shift data...
Abstract Motivation The generation of parameter files for molecular dynamics (MD) simulations small molecules that are suitable force fields commonly applied to proteins and nucleic acids is often challenging. ACPYPE software website aid the such files. Results uses OpenBabel ANTECHAMBER generate MD input in Gromacs, AMBER, CHARMM, CNS formats. It can now take a SMILES string as input, addition original PDB or mol2 coordinate files, with GAFF2 support GLYCAM field conversion added. be...
The WeNMR ( http://www.wenmr.eu ) project is a European Union funded international effort to streamline and automate analysis of Nuclear Magnetic Resonance (NMR) Small Angle X-Ray scattering (SAXS) imaging data for atomic near-atomic resolution molecular structures. Conventional calculation structure requires the use various software packages, considerable user expertise ample computational resources. To facilitate NMR spectroscopy SAXS in life sciences consortium has established standard...
High-throughput sequencing methods are generating enormous amounts of genomic data, giving unprecedented insights into human genetic variation and its relation to disease. An individual genome contains millions Single Nucleotide Variants: discriminate the deleterious from benign ones, a variety have been developed that predict whether protein-coding variant likely affects carrier individual's health. We present such method, DEOGEN2, which incorporates heterogeneous information about...
Protein dynamics are important for understanding protein function. Unfortunately, accurate information is difficult to obtain: here we present the DynaMine webserver, which provides predictions fast backbone movements of proteins directly from their amino-acid sequence. rapidly produces a profile describing statistical potential such at residue-level resolution. The predicted values have meaning on an absolute scale and go beyond traditional binary classification residues as ordered or...
We present a suite of programs, named CING for Common Interface NMR Structure Generation that provides residue-based, integrated validation the structural ensemble in conjunction with experimental restraints and other input data. External programs new internal routines compare NMR-derived models empirical data, measured chemical shifts, distance- dihedral results are visualized dynamic Web 2.0 report. A red–orange–green score is used residues to direct user those critiques warrant further...
Abstract The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural functional annotations of macromolecular structure data, contained the (PDB). goal PDBe-KB two-fold: (i) to increase visibility reduce fragmentation contributed by specialist data resources, make these more findable, accessible, interoperable reusable (FAIR) (ii) place their...
Disulfide bonds are crucial for many structural and functional aspects of proteins. They have a stabilizing role during folding, can regulate enzymatic activity trigger allosteric changes in the protein structure. Moreover, knowledge topology disulfide connectivity be relevant genomic annotation tasks provide long range constraints ab-initio structure predictors. In this paper we describe PhyloCys, novel unsupervised predictor bond from known cysteine oxidation states. For each query...
The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the (PDB). goal of PDBe-KB place macromolecular structure their biological context by developing standardised exchange formats integrating partner into a knowledge graph that can provide valuable insights. Since we described 2019, there have been significant...
Abstract Deep mutational scanning is a powerful approach to investigate wide variety of research questions including protein function and stability. Here, we perform deep on three essential E. coli proteins (FabZ, LpxC MurA) involved in cell envelope synthesis using high-throughput CRISPR genome editing, study the effect mutations their original genomic context. We use more than 17,000 variants interrogate importance individual amino acids supporting viability. Additionally, exploit these...
Abstract Intrinsic disorder (ID) in proteins is well-established structural biology, with increasing evidence for its involvement essential biological processes. As measuring dynamic ID behavior experimentally on a large scale remains difficult, scores of published predictors have tried to fill this gap. Unfortunately, their heterogeneity makes it difficult compare performance, confounding biologists wanting make an informed choice. To address issue, the Critical Assessment protein Disorder...