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AXES / Analysis of X-ray Scattering in Explicit Solvent
Fits small angle X-ray scattering (SAXS) data to macromolecular structures and ensembles of structures. AXES is a web application using a Powell minimization of the penalty function against the adjustable parameters for both experimental and predicted data. The software allows the prediction of solution X-ray scattering data for a macromolecule in explicit aqueous solvent and calculation of the best fit between the experimental scattering data and a structural model.
PyFAI / Python For Fast Azimuthal Integration
Performs azimuthal integration and two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments. PyFAI is a software package and library that implements various integration algorithms, including multiple-pixel splitting schemes. The software can be used to decompose diffraction images into amorphous and crystalline components. Users can incorporate the pyFAI library into their processing pipeline or into other tools like PyMca and EDNA.
AquaSAXS
Allows structural biologists to compare their SAXS data to the theoretical one for a model given as a PDB or PQR file. AquaSAXS takes advantage of recently developed methods, such as AquaSol, that give the equilibrium solvent density map around macromolecules, to compute an accurate SAXS/WAXS profile of a given structure and to compare it to the experimental one. AquaSAXS provides a way for the user to check and/or tune the atomic types and the corresponding parameters that are used for computing the solute and the solvent-excluded-volume contribution to the SAXS profile.
WAXSiS / WAXS in solvent
Computes small- and wide-angle X-ray scattering curves based on explicit-solvent all-atom molecular dynamics simulations. Unlike other web servers, WAXSiS is based on explicit-solvent molecular dynamics simulations. Thus, WAXSiS uses a highly accurate model for the hydration layer of the biomolcules and for the excluded solvent. In addition, the simulations account for thermal fluctuations of water, side chains, and counter ions. WAXSiS does not require any fitting parameters associated with the hydration layer or excluded solvent, rendering the calculations highly predictive.
pyDockSAXS
A web server for rigid-body protein-protein docking that combines computational and experimental information. On one side the server uses the new version of pyDock (pyDock 3.0) to energetically evaluate the interaction surface of multiple docking poses. On the other side, the server evaluates the capacity of each pose to describe the experimental curve of SAXS with the program CRYSOL. The appropriate combination of both scoring functions yields predictions of the 3D arrangement of the complex in solution.
SASpy
A PyMOL plugin that provides an easy-to-use graphical interface for SAXS-based hybrid modeling. Through a few mouse clicks in SASpy, low-resolution models can be superimposed to high-resolution structures, theoretical scattering profiles and fits can be calculated and displayed on-the-fly. Mouse-based manual rearrangements of complexes are conveniently applied to rapidly check and interactively refine tentative models. Interfaces to automated rigid-body and flexible refinement of macromolecular models against the experimental SAXS data are provided.
DARA
A web-server, that queries over 150 000 scattering profiles pre-computed from the high resolution models of macromolecules and biological assemblies in the Protein Data Bank (PDB), to rapidly find nearest neighbours of a given experimental or theoretical small angle X-ray scattering (SAXS) pattern. Identification of the best scattering equivalents provides a straightforward and automated way of structural assessment of macromolecules based on a SAXS profile. DARA results are useful e.g. for fold recognition and finding of biologically active oligomers.
Fast-SAXS
A software tool for small-angle X-ray scattering of proteins. The Fast-SAXS method is built within the framework of the Debye formalism. Notably, in addition to the introduction of CG structure factors for amino acids, explicit CG water molecules are placed at the protein surface to account for the collective scattering contributions. Fast-SAXS takes advantage of the intrinsic low-resolution and CG nature of solution scattering data. It allows rapid scattering determination from a large number of conformations that can be extracted from CG simulations to obtain scattering characterization of protein conformations. The method includes three important elements, (1) effective residue structure factors derived from the Protein Data Bank, (2) explicit treatment of water molecules in the hydration layer at the surface of the protein, and (3) an ensemble average of scattering from a variety of appropriate conformations to account for macromolecular flexibility (At the moment, the ensemble generation is up to users).
SAXSTER
Uses small-angle x-ray scattering (SAXS) data to improve template-based protein structure prediction. The strategy first extracts the SAXS profiles from Cα-based template alignments using an extended CG SAXS model. The intensity profile of each template is then matched with the SAXS data of the target proteins to prioritize the template proteins with a SAXS profile similar to that of the target. We achieved the best template recognition results when we combined the SAXS profile score with the original threading alignment scores.
SASfit
Allows users to analyze and plot small angle scattering data. SASfit is a program developed for model-based analysis of small-angle scattering (SAS) data, with an interface lowering the barrier of entry. The software contains over 200 models for fitting and enables calculation of integral structural parameters and fitting size distributions together with several form factors. It includes (1) algorithms to reduce oversampled data sets, and (2) a plug-in system for custom user-provided models.
CRYSOL
A program for evaluating the solution scattering from macromolecules with known atomic structure and fitting it to experimental scattering curves from Small-Angle X-ray Scattering (SAXS). CRYSOL uses multipole expansion of the scattering amplitudes to calculate the spherically averaged scattering pattern and takes into account the hydration shell. Given SAXS experimental data, CRYSOL can fit the theoretical scattering curve by minimizing the discrepancy (chi-square value). Fitting is done by varying three parameters: (i) average displaced solvent volume per atomic group (ii) contrast of the hydration shell (iii) relative background.
MaxOcc / Maximum Occurrence
Permits users to prepare and run calculations. MaxOcc hides complexity of the interaction with the grid. Its calculations are run on the WeNMR grid, allowing a few hundred conformations to be analyzed simultaneously. This tool accepts as input data both paramagnetic Nuclear Magnetic Resonance (NMR) data (pcs, rdc and/or pre data) and Small-Angle X-ray Scattering (SAXS) profiles. It streamlines preparation of input data and the retrieval and analysis of the calculation results.
DIOPTAS
Enables reduction of two-dimensional X-ray diffraction (XRD) data and data exploration. DIOPTAS is a program developed for on-the-fly data processing and analysis for all kinds of experiments, either online at Large Scale Facilities or home laboratories. The software is divided into three general parts: the calibration module, the mask module and the integration/analysis module. It also includes capabilities for processing XRD data collected at high pressures and/or high temperatures.
pySAXS / Python for Small Angle X-ray Scattering
Offers a set of functions dedicated to Small Angle X-ray Scattering (SAXS) data treatment. pySAXS is a modulable application working with plugins systems. It performs deconvolution or background substraction as well as computation of model SAXS intensities. The software is available as both a command-line program or as a graphical user interface called guisaxs. It also can be integrated in scripts for automatizing calculation or its librairies and models can be used in programs.
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