Software

Structural Analysis

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. The software algorithm allows for improved handling of difficult situations like highly transparent crystals, ba...

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Platforms
  • Linux
  • Windows
License
  • Academic
  • Commercial
Structural Analysis

Agadir

Agadir 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...

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  • (not defined)
Structural Analysis

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. The latter attempts to mimic...

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  • (not defined)
Structural Analysis

ATSAS

ATSAS is a program suite for small angle scattering (SAS) data analysis and modelling. Small angle scattering of X-rays (SAXS) and neutrons (SANS) is widely used to study the structure of biological macromolecules in solution and non-biological iso...

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Platforms
  • Linux
  • Mac
  • Windows
License
  • (not defined)
Structural Analysis

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. It is a program for calculating the folding pathways of proteins and for c...

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  • (not defined)
Structural Analysis

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 ...

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  • (not defined)
Structural Analysis

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. This prediction is based on straightforward empirical rules which are applied to the sequenc...

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Platforms
  • Windows
License
  • Academic
  • Commercial
Structural Analysis

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 bu...

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  • (not defined)
Structural Analysis

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. The software is based on the presumpti...

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  • (not defined)
Systems Biology

SmartCell

SmartCell provides information about the evolution of a network in one cell. It has been developed to be a general framework for modelling and simulation of diffusion-reaction networks in a whole-cell context. It supports localisation and diffusion b...

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Embassy Cloud

EMBL-EBI Embassy Cloud is a service that enables data analysis activities alongside EBI public datasets in a secure, private virtual datacenter, with flexible configuration, tailored to each tenant’s requirements. The Embassy Cloud provides EMBL-EB...

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  • (not defined)
Imaging

AutoFocusScreen for ZEN

AutoFocusScreen for ZEN allows intuitive set-up of complex time-lapse experiments for Zeiss confocal microscopes. AutoFocusScreen for ZEN is a VBA macro that allows intuitive set-up of complex time-lapse and multiposition experiments for Zeiss confo...

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Platforms
  • Windows
License
  • Academic
  • Commercial
Imaging

Micropilot

Micropilot is a microscopy software that can be rapidly trained to identify cells of interest automatically and automate even complex fluorescence microscopy-based imaging assays. Micropilot can be rapidly trained by the user to identify objects in a...

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Platforms
  • Windows
License
  • Academic
  • Commercial
Protein-Function Analysis

SMART

SMART (Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 500 domain families found in signalling, extracellular and chromatin-associat...

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Platforms
  • Linux
  • Windows
License
  • Academic
  • Commercial
Protein-Function Analysis

SNPeffect

SNPeffect is a database of human non-synonymous coding SNPs (nsSNPs) mapping phenotypic effects of allelic variation in human genes. SNPeffect contains 31 659 nsSNPs from 12 480 human proteins. The current release of SNPeffect incorporates data on pr...

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  • (not defined)
Protein-Function Analysis

STRING

STRING is a database of interactions between proteins - essentially, it is a platform for system-level exploration of cellular machineries. Experimental interaction evidence from a diverse collection of repositories is integrated at a single location...

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  • (not defined)
Instrument Control

StaubCom

StaubCom is a Val3 library designed to facilitate the integration of Stäubli robots into high level control systems. The framework can be installed on Stäubli CS8C robot controllers. It runs a generic socket server implementing the StaubCom string b...

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Platforms
  • Online tool
License
  • Academic
Instrument Control

JLib

JLib provides a framework and components designed to simplify the development, deployment and maintenance of reliable instrument control software. Jlib has been in use since 2007 at EMBL-Grenoble and is an essential part of several commercially avail...

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Platforms
  • Linux
  • Mac
  • Windows
License
  • Academic
  • Commercial

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