A5033074461- Research Data Management Practices
- Scientific Computing and Data Management
- Enzyme Structure and Function
- Protein Structure and Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Data Quality and Management
- Analytical Chemistry and Chromatography
- Crystallography and molecular interactions
- Molecular spectroscopy and chirality
- Crystallization and Solubility Studies
- Semantic Web and Ontologies
- Big Data and Business Intelligence
- X-ray Diffraction in Crystallography
- Medical Imaging Techniques and Applications
- Computational Drug Discovery Methods
- Spectroscopy and Quantum Chemical Studies
- Biomedical Text Mining and Ontologies
- RNA and protein synthesis mechanisms
- Protein Tyrosine Phosphatases
- Crystal structures of chemical compounds
- Mass Spectrometry Techniques and Applications
- Free Radicals and Antioxidants
- Advanced Biosensing Techniques and Applications
- Biochemical and Molecular Research
- Biotin and Related Studies
Center for Life Sciences
2016-2021
Vrije Universiteit Amsterdam
2019-2020
Netherlands Bioinformatics Centre
2010-2019
Netherlands eScience Center
2015-2019
Dutch Techcentre for Life Sciences
2017-2019
Delaware Division of Libraries
2016
Radboud University Medical Center
2010-2011
Utrecht University
1990-2011
Radboud University Nijmegen
2010-2011
University Medical Center Groningen
2011
There is an urgent need to improve the infrastructure supporting reuse of scholarly data. A diverse set stakeholders-representing academia, industry, funding agencies, and publishers-have come together design jointly endorse a concise measureable principles that we refer as FAIR Data Principles. The intent these may act guideline for those wishing enhance reusability their data holdings. Distinct from peer initiatives focus on human scholar, Principles put specific emphasis enhancing ability...
The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series databases that run parallel to PDB. Each database holds one entry, if possible, for each PDB entry. DSSP secondary proteins. PDBREPORT reports on quality and lists errors. HSSP multiple sequence alignment all PDBFINDER easy parse summaries file content, augmented with essentials from other systems. PDB_REDO re-refined, often improved, copies structures solved by X-ray....
A new probabilistic approach is introduced for the determination of absolute structure a compound which known to be enantiopure based on Bijvoet-pair intensity differences. The method provides relative probabilities different models chiral composition structure. outcome this type analysis can also cast in form value, along with associated standard uncertainty, that resembles value well Flack x parameter. uncertainty we obtain often about half proposed formalism suited particular...
The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 guiding do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability Reusability digital resources. This has likely contributed to adoption principles, because individual stakeholder communities can implement own solutions. However, it also resulted inconsistent...
MotivationStatistical methods that compare observed and expected distributions of experimental observables provide powerful tools for the quality control protein structures. The distribution backbone dihedral angles ('Ramachandran plot') has often been used such control, but without a firm statistical foundation.
A method is presented that positions polar hydrogen atoms in protein structures by optimizing the total bond energy. For this goal, an empirical force field was derived from small molecule crystal structures. Bifurcated bonds are taken into account. The procedure also predicts ionization states of His, Asp, and Glu residues. During optimization, sidechain conformations Gln, Asn residues allowed to change their last χ angle 180° compensate for crystallographic misassignments. Crystal...
A procedure is described, for an Eulerian or Kappa goniostat, to determine the exact spindle value φ at moment of impact a reflection on area detector; such information essential calculation accurate vectors and, eventually, unit-cell and lattice orientation. The method based comparison coordinates two related images. One image obtained by rotation over few degrees (`φ scan') other same rotation, but with superposed (χ) perpendicular first (`φ/χ scan'). In both cases, kept primary beam, i.e....
Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does aim to propose new development best practices, but rather provide simple recommendations encourage the adoption of existing practices. Software promote better improves reproducibility reusability research. These are designed around Open Source values, practical suggestions contribute making source code more discoverable,...
A novel way has been developed for using the umbrella potential method of calculating mean force molecular dynamics. During a simulation, is improved periodically, taking into account all results obtained previously. The was tested by determination central dihedral angle in glycol (as molecule vacuo and solutions water CCl4). Advantages over other methods are that relatively small amount manual intervention necessary an intermediate result after simulation time already complete, although...
Abstract In this study we concentrate on replacing side chains as a subtask of model building by homology. Two problems arise. How to determine potential low energy rotamers? And how avoid the combinatorial explosion that results from combination many residues for which multiple good rotamers are predicted? We attempt solve these choosing position‐specific rather than generalized and sorting have be modelled function their freedom in rotamer space. The practical advantages our method quality...
MotivationThe Protein Data Bank currently contains more than 4700 protein coordinate sets. It is often desirable to make a selection from these files based on criterion like R-factor, experimental method, length of the amino acid sequence, or number homologous sequences in swissprot. Doing this using distributed form can be tedious task, because (1) requires reading one file for every single entry, and (2) not all information present consistent computer readable way entries.
The previously described method for absolute structure determination [Hooft, Straver & Spek (2008). J. Appl. Cryst. 41 , 96–103] assumes a Gaussian error distribution. is now extended to make it robust against poor data with large systematic errors the introduction of Student t -distribution. It shown that this modification makes very little difference good but dramatically improves results non-Gaussian
Electrostatic interactions play a key role in many aspects of protein engineering. Consequently, much effort has been put into the design software for calculating electrostatic fields around macromolecules. We show that optimization hydrogen bonding networks can improve both results pK(a) calculations and performed by commonly used programs such as DelPhi. Further often be achieved flipping side chains asparagine, histidine glutamine their chi2, chi2 chi3 torsion angles, respectively, when...
The Data Stewardship Wizard is a tool for data management planning that focused on getting the most value out of project itself rather than fulfilling obligations. It based FAIR Stewardship, in which each data-related decision acts to optimize Findability, Accessibility, Interoperability and/or Reusability data. background this philosophy first reuser researcher themselves. encourages consulting expertise and experts, can help researchers avoid risks they did not know would encounter by...
Nine of the 20 natural amino acids contain a planar group in their side chains. For these groups, normal deviations from planarity were derived by study similar fragments accurately determined small molecule structures. Comparison with values found representative set high-quality protein structures revealed that aromatic residues and arginine is comparable to molecules. Asn, Gin, Asp Glu, however, are up twice as large small-molecule structures, suggesting adding an extra restraint for...
Crystal engineering of melamine -imide complexes: tuning the stoichiometry by steric hindrance imide carbonyl groups
Effective stewardship of data is a critical precursor to making FAIR. The goal this paper bring an overview current state the art management and planning solutions (DMP). We begin by arguing why important vehicle supporting adoption implementation FAIR principles, we describe background, context historical development, as well major driving forces, being research initiatives funders. Then provide leading DMP tools in form table presenting key characteristics. Next, elaborate on emerging...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular dynamics study of conformational and anomeric equilibria in aqueous D-glucoseBouke P. van Eijck, Rob W. Hooft, Jan KroonCite this: J. Phys. Chem. 1993, 97, 46, 12093–12099Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/j100148a041https://doi.org/10.1021/j100148a041research-articleACS PublicationsRequest reuse permissionsArticle...
Abstract Study of the most conserved region in many β/α‐barrels, phosphate‐binding site, revealed a sequence motif few β/α‐barrels with known tertiary structure, namely glycolate oxidase (GOX), cytochrome b 2 (Cyb2), tryptophan synthase α subunit (TrpA), and indoleglycerolphosphate (TrpC). Database searches identified this numerous other enzyme families: (1) IMP dehydrogenase (IMPDH) GMP reductase (GuaC); (2) phosphoribosylformimino‐5‐aminoimidazol carboxamide ribotide isomerase (HisA)...