EMBL News 2013
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Agadir

Agadir is a prediction algorithm based on the helix/coil transition theory. Agadir predicts the helical behaviour of monomeric peptides. » DetailsAgadir is a prediction algorithm based on the helix/coil transition theory. Agadir predicts the helical behaviour of monomeric peptides. It only considers short range interactions. Conditions such as pH, temperature and ionic strength are used in the calculation. Modifications of the termini are also allowed. However, Agadir is not a program to predict secondary structure of proteins. 1200 peptides were analysed to evaluate the performance of the algorithm. The average deviation of the prediction from experimental values (obtained from CD measurements) is -2 percent of helical content, with a standard deviation of 6 (percent of helical content). i.e., a peptide with 30% helix content would be predicted to have 28%+-6%.

If you want to obtain more information please contact us at info@embl-em.de

Arp/Warp

The Automated Refinement Procedure, ARP/wARP is a program package for protein structure refinement. It combines in an iterative manner reciprocal space structure factor refinement with updating of the model in real space. » DetailsThe Automated Refinement Procedure, ARP/wARP is a program package for protein structure refinement. It combines in an iterative manner reciprocal space structure factor refinement with updating of the model in real space. The latter attempts to mimic and automate a typically time extensive model rebuilding session at the graphics. The real space update utilises some general properties of the electron density synthesis as well as stereo-chemical criteria. The ARP/wARP suite is under continuous development.

If you want to obtain more information please contact us at info@embl-em.de

C3D

C3D is a software to automatically locate a crystal and its holder for centring on a goniometer spindle and alignment with an X-ray beam. » DetailsC3D is a software to automatically locate a crystal and its holder for centring on a goniometer spindle and alignment with an X-ray beam. The software algorithm allows for improved handling of difficult situations like highly transparent crystals, bad cryo-cooling or lens effects arising from the geometry of the drop.

The C3D program is designed to operate with a client program that controls specific diffractometer hardware. In order to select the best detection conditions, C3D provides various functionalities adapted to various hardware configurations.

Downloads available:
v3.9.7.1 for Windows (commercial)Full package including C3D shell command and Matlab libraries. New version 3.9.7.1 comprising the following features: - corrections loop centre detection failure - loop detection much more robust at low zoom level. Correlation between images used like in crystal detection. - crystal detection slightly optimized - better management of inhomogeneous backgrounds
v3.9.7.1 for Windows (Academic)Full package including C3D shell command and Matlab libraries. New version 3.9.7.1 comprising the following features: - corrections loop centre detection failure - loop detection much more robust at low zoom level. Correlation between images used like in crystal detection. - crystal detection slightly optimized - better management of inhomogeneous backgrounds
v3.9.7.1 for Linux (commercial)Full package including C3D shell command and Matlab libraries. New version 3.9.7.1 comprising the following features: - corrections loop centre detection failure - loop detection much more robust at low zoom level. Correlation between images used like in crystal detection. - crystal detection slightly optimized - better management of inhomogeneous backgrounds
v3.9.7.1 for Linux (Academic)Full package including C3D shell command and Matlab libraries. New version 3.9.7.1 comprising the following features: - corrections loop centre detection failure - loop detection much more robust at low zoom level. Correlation between images used like in crystal detection. - crystal detection slightly optimized - better management of inhomogeneous backgrounds

PolyPhen

PolyPhen (=Polymorphism Phenotyping) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein. » DetailsPolyPhen (=Polymorphism Phenotyping) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein. This prediction is based on straightforward empirical rules which are applied to the sequence, phylogenetic and structural information characterizing the substitution. PolyPhen prediction specifically focuses on non-synonymous SNPs (nsSNPs), i.e. SNPs located in coding regions and resulting in amino acid variation in protein products of genes.

Downloads available:
1.13 (Commercial)V1.13
1.13 (Academic)V1.13

TANGO

The TANGO software allows to predict protein aggregation based on a statistical mechanics algorithm. It is based on the physico-chemical principles of beta-sheet formation, extended by the assumption that the core regions of an aggregate are fully buried. » DetailsThe TANGO software allows to predict protein aggregation based on a statistical mechanics algorithm. It is based on the physico-chemical principles of beta-sheet formation, extended by the assumption that the core regions of an aggregate are fully buried. The algorithm accurately predicts the aggregation of a data set of 179 peptides compiled from the literature as well as of a new set of 71 peptides derived from human disease-related proteins, including prion protein, lysozyme and beta2-microglobulin. Tango sets the stage for fully automated, sequence-based design strategy to improve the aggregation properties of proteins of scientific or industrial interest.

If you want to obtain more information please contact us at info@embl-em.de

FOLD-X

FOLD-X is an algorithm which provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. » DetailsFOLD-X is an algorithm which provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. It is a program for calculating the folding pathways of proteins and for calculating the effect of a point mutation on the stability of a protein. The predictive power of FOLD-X has been tested on a very large set of point mutants (1088 mutants) spanning most of the structural environments found in proteins. FOLD-X uses a full atomic description of the structure of the proteins. The different energy terms taken into account in FOLD-X have been weighted using empirical data obtained from protein engineering experiments.

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Dali (MaxSprout)

The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. » DetailsThe Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is mailed back to you. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. If you want to know the structural neighbours of a protein already in the Protein Data Bank, you can find them in the FSSP database.

If you want to obtain more information please contact us at info@embl-em.de

ATSAS

ATSAS - software for small angle scattering data analysis from biological macromolecules. ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules. » DetailsATSAS - software for small angle scattering data analysis from biological macromolecules. ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules. It has been developed for small angle X-ray and neutron scattering data analysis. The package includes a number of computer programs primarily oriented towards analysis of biological macromolecules, but they can also be used for non-biological isotropic and partially ordered objects (inorganic, colloidal solutions, polymers in solution and bulk). The software system covers all the analysis steps from data reduction to automated modeling methods, and includes computational modules as well as 3D graphics visualization software. Most of the programs can be invoked from a menu-driven graphical user interface implemented in the package PRIMUS. The programs at different stages of data analysis can also be run individually in automated or interactive modes.

If you want to obtain more information please contact us at info@embl-em.de

InterPreTs

InterPreTs Interaction Prediction through Structure. InterPreTs is a program to test putative interactions on complexes of known three dimensional (3D) structure, determined by experimental structural biology methods such as X-ray crystallography or NMR. » DetailsInterPreTs Interaction Prediction through Structure. InterPreTs is a program to test putative interactions on complexes of known three dimensional (3D) structure, determined by experimental structural biology methods such as X-ray crystallography or NMR. Given a 3D complex and alignments of homologues of the interacting proteins, the program assesses the fit of any possible interacting pair on the complex using empirical potentials. For studies of interacting protein families that show different specificities, the method provides a ranking of interacting pairs useful for prioritising experiments.

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ViCi

ViCi -for in silico ligand-based drug design - employs shape matching methodologies and dovetails them with further tools that help to describe the atomic makeup of a molecule and its electrostatic distribution. » DetailsViCi -for in silico ligand-based drug design - employs shape matching methodologies and dovetails them with further tools that help to describe the atomic makeup of a molecule and its electrostatic distribution. The software is based on the presumption that molecules of a similar size, shape and atomic makeup should interact with protein binding pockets in similar manners. Given a known macromolecular ligand, it should be possible to extract similar molecules from a large database that would interact with that molecule in a similar way, and crucially, with more affinity in some cases. The improvements in affinity can arise from the forming of new contacts, the probing of unused pockets within a binding site or the altering of molecular substructure in order to reduce conformational variability within the ligand, and the software can probe all such changes in an extremely short time-scale (a database of 8 million compounds can be screened in a few hours on a single CPU core). The newly discovered ligands should be candidates for drug development and further investigations going forward. For further information you may also visit the ViCi srever at the EMBL Hamburg at http://cluster.embl-hamburg.de/vici/cgi-bin/vici.

If you want to obtain more information please contact us at info@embl-em.de