A5081712139- Enzyme Structure and Function
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Biochemical and Molecular Research
- RNA modifications and cancer
- Glycosylation and Glycoproteins Research
- Bacteriophages and microbial interactions
- RNA Research and Splicing
- Bacterial Genetics and Biotechnology
- Monoclonal and Polyclonal Antibodies Research
- Mass Spectrometry Techniques and Applications
- Advanced NMR Techniques and Applications
- Ubiquitin and proteasome pathways
- Nanoparticle-Based Drug Delivery
- X-ray Spectroscopy and Fluorescence Analysis
- Protein purification and stability
- Lipid Membrane Structure and Behavior
- Photosynthetic Processes and Mechanisms
- DNA and Nucleic Acid Chemistry
- Cardiomyopathy and Myosin Studies
- X-ray Diffraction in Crystallography
- Advanced biosensing and bioanalysis techniques
- Protein Kinase Regulation and GTPase Signaling
- DNA Repair Mechanisms
- Genomics and Chromatin Dynamics
European Molecular Biology Laboratory
2016-2025
Deutsches Elektronen-Synchrotron DESY
2014-2024
European Molecular Biology Laboratory
2014-2023
SIB Swiss Institute of Bioinformatics
2022
King's College London
2021
D.I. Ivanovsky Institute of Virology Russian Academy of Medical Sciences
2018-2021
Ministry of Health of the Russian Federation
2018-2021
University of Freiburg
2021
European Bioinformatics Institute
2003-2019
A.V. Shubnikov Institute of Crystallography
2002-2018
A method is proposed for the determination of optimum value regularization parameter (Lagrange multiplier) when applying indirect transform techniques in small-angle scattering data analysis. The based on perceptual criteria what best solution. set simple used to construct a total estimate describing quality Maximization straightforward. Model computations show effectiveness technique. implemented program GNOM [Svergun, Semenyuk & Feigin (1988). Acta Cryst. A44, 244–250].
A program for evaluating the solution scattering from macromolecules with known atomic structure is presented. The uses multipole expansion fast calculation of spherically averaged pattern and takes into account hydration shell. Given coordinates (e.g. Brookhaven Protein Data Bank) it can either predict curve or fit experimental using only two free parameters, average displaced solvent volume per group contrast layer. runs on IBM PCs major UNIX platforms.
A program suite for one-dimensional small-angle scattering data processing running on IBM-compatible PCs under Windows 9 x /NT/2000/XP is presented. The main program, PRIMUS , has a menu-driven graphical user interface calling computational modules to perform manipulation and analysis. Experimental in binary OTOKO format can be reduced by the SAPOKO which includes statistical analysis of time frames, averaging scaling. Tools generate angular axis detector response files from diffraction...
DAMMIF, a revised implementation of the ab-initio shape-determination program DAMMIN for small-angle scattering data, is presented. The was fully rewritten, and its algorithm optimized speed execution modified to avoid limitations due finite search volume. Symmetry anisometry constraints can be imposed on particle shape, similar DAMMIN. In equivalent conditions, DAMMIF 25-40 times faster than single CPU. possibility utilize multiple CPUs added DAMMIF. application available in binary form...
New developments in the program package
Scattering patterns from geometrical bodies with different shapes and anisometry (solid hollow spheres, cylinders, prisms) are computed the reconstructed ab initio using envelope function bead modelling methods. A procedure is described to analyze multiple solutions provided by modeling methods estimate stability reliability of shape reconstruction. It demonstrated that flat more difficult restore than elongated ones types indicated, which require additional information for reliable...
ATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions biological macromolecules or nanoparticles. It contains applications primary processing and assessment, ab initio bead modelling, model validation, as well methods flexibility mixtures. In addition, approaches are supported that utilize information X-ray crystallography, nuclear magnetic resonance spectroscopy atomistic homology modelling to construct hybrid models based on data....
A method is presented for automated best-matching alignment of three-dimensional models represented by ensembles points. normalized spatial discrepancy (NSD) introduced as a proximity measure between objects. Starting from an inertia-axes alignment, the algorithm minimizes NSD; final value NSD provides quantitative estimate similarity The implemented in computer program. Simulations have been performed to test its performance on model structures with specified numbers points ranging few...
Structural analysis of flexible macromolecular systems such as intrinsically disordered or multidomain proteins with linkers is a difficult task high-resolution techniques are barely applicable. A new approach, ensemble optimization method (EOM), proposed to quantitatively characterize in solution using small-angle X-ray scattering (SAXS). The flexibility taken into account by allowing for the coexistence different conformations protein contributing experimental pattern. These conformers...
Small-angle scattering (SAS) of x-rays and neutrons is a fundamental tool in the study biological macromolecules. The major advantage method lies its ability to provide structural information about partially or completely disordered systems. SAS allows one structure native particles near physiological environments analyse changes response variations external conditions.
The structure of the protein–solvent interface is subject controversy in theoretical studies and requires direct experimental characterization. Three proteins with known atomic resolution crystal (lysozyme, Escherichia coli thioredoxin reductase, protein R1 E. ribonucleotide reductase) were investigated parallel by x-ray neutron scattering H 2 O D solutions. analysis based on significantly different contrasts for hydration shell. results point to existence a first shell an average density...
The
The Fortran program package GNOM carries out SAS data treatment and interpretation for the disperse non-interacting dilute systems of different types. A general operator method based on Tikhonov's regularization technique is used. Here a finite real-space distribution function [the correlation p(r) monodisperse size D(R) polydisperse ones] searched to fit experimental in accordance with conditions error bounds. It possible require non-negativity solution. applicable arbitrary (arbitrary...
The program package ATSAS 2.1 for small-angle X-ray and neutron scattering data analysis is presented. programs included in the cover major processing interpretation steps from primary reduction to three-dimensional modelling. This system primarily oriented towards of biological macromolecules, but could also be used non-biological isotropic partially ordered objects (nanoparticle systems, colloidal solutions, polymers solution bulk). Recent developments are highlighted. main run on multiple...
Dynamic ensembles of macromolecules mediate essential processes in biology. Understanding the mechanisms driving function and molecular interactions 'unstructured' flexible molecules requires alternative approaches to those traditionally employed structural Small-angle X-ray scattering (SAXS) is an established method for characterization biological solution, directly applicable study systems such as intrinsically disordered proteins multi-domain with unstructured regions. The Ensemble...
A high-brilliance synchrotron P12 beamline of the EMBL located at PETRA III storage ring (DESY, Hamburg) is dedicated to biological small-angle X-ray scattering (SAXS) and has been designed optimized for experiments on macromolecular solutions. Scatterless slits reduce parasitic scattering, a custom-designed miniature active beamstop ensures accurate data normalization photon-counting PILATUS 2M detector enables background-free detection weak signals. The high flux small beam size allow...
Small-angle scattering (SAS) is frequently employed for screening large numbers of samples and studying these under different conditions, including space- time-resolved analysis. These measurements produce immense amounts data, especially on modern high-flux high-brilliance sources (e.g. third-generation synchrotrons). In biological SAS, like high-throughput macromolecular crystallography, large-scale analysis proteins complexes also emerging. Automation data becomes an indispensable...