Software Directory

Software package ANAELU (analytical emulator Laue utility) has been created for aiding the interpretation of two-dimensional X-ray diffraction patterns produced by textured (bulk and nanostructured) samples. ANAELU is composed of three interconnected applications, corresponding to three crystallographic tasks: structure representation, two-dimensional pattern analysis and diffraction simulation.

The program determines anomalous (or heavy-atom) densities by reversing the usual procedure for experimental phase determination. Instead of adding a phase shift to the heavy-atom phases to obtain a starting value for the native protein phase, this phase shift is subtracted from the native phase to obtain the heavy-atom substructure phase.

Analysis of NMR spectra. Tool for analysis and assignment of multidimensional spectra.

Protein analysis. Web on-line tool.

Modelling amorphous structures by a Rietveld-type refinement of the atomic coordinates.

ARP/wARP is used for automated building and refinement of protein structures. Real space pattern recognition, refinement and model update are combined with reciprocal space refinement to construct and improve protein models. ARP/wARP can also be used for ab initio structure solution of metalloproteins at high resolution.

Ascalaph is a general purpose molecular modeling suite that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics simulations in the gas or in condensed phase. It can interact with external molecular modeling packages (MDynaMix, NWChem, CP2K and PC GAMESS/Firefly).

For the generation and calculation of the X-ray structure factors and the real and imaginary parts of the structure factors of any crystalline system.

For the generation and calculation of the X-ray structure factors and the real and imaginary parts of the structure factors of any crystalline system.

The program takes a multiple protein sequence alignment and estimates the range in accuracy that one can expect for a "perfect" secondary structure prediction made using the alignment.

This software package is based on the IFEFFIT library of numerical and XAS algorithms. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demands of an expert practitioner.

atomes is a cross-platform open source program developed to analyze, to visualize and to edit/create large three-dimensional atomic scale models.
By regrouping advanced analysis techniques, 3D visualization and 3D edition, atomes introduces innovative 3D rendering possibilities and intuitive applications of the calculation results.
atomes also provides an advanced input preparation system for further calculations using well known classical, ab-initio and QM-MM molecular dynamics codes.
To prepare the input files for these calculations is likely to be the key, and most complicated step towards MD simulations.atomes offers a user-friendly assistant to help and guide the user step by step to achieve this crucial goal.

Display of atomic structures.

New developments in version 2.4 of the ATSAS package for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described.

Automates many of the computational steps involved in using X-PLOR.

Autodep is a tool designed for the deposition into the Protein Data Bank of molecular coordinates data generated by the experimental procedures, viz. protein crystallography, NMR, EM.

Suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Of use for X-ray crystallography, structure-based drug design, lead optimization, virtual screening (HTS), combinatorial library design, protein-protein docking, chemical mechanism studies.

Program for X-ray powder diffraction data evaluation that is specially designed for peak-shape analysis and data preparation for Rietveld refinement in connection with the FULLPROF program.

Analysis of NMR spectra. Suite of programs for the processing of multidimensional spectra

Program designed to interconvert a number of file formats currently used in molecular moldeling. rpm for Linux available at ftp site.