Who is Using OpenStructure?

SWISS-MODEL - Expert System for Protein Structure Modelling

SWISS-MODEL is a widely used automated protein structure homology-modelling server for generating three-dimensional models of a protein. SWISS-MODEL automates the complex process of model building on an easy to use web based system, thereby making model information available also for non-specialists.

Project Website

SWISS-MODEL Repository - Database of 3D Protein Structure Models for UniProtKB

The aim of the SWISS-MODEL Repository is to provide access to an up-to-date collection of annotated 3D protein models generated by automated homology modelling for relevant model organisms and experimental structure information for all sequences in UniProtKB. Regular updates ensure that target coverage is complete, that models are built using the most recent sequence and template structure databases, and that improvements in the underlying modelling pipeline are fully utilised. It also allows users to assess the quality of the models using the latest QMEAN results. If a sequence has not been modelled, the user can build models interactively via the SWISS-MODEL workspace.

Project Website

CAMEO - Continuous Automated Model EvaluatiOn

CAMEO is a community-wide project, running since January 2012, intended as complement to the bi-annual CASP experiment. CAMEO relies on the weekly PDB pre-release and performs a fully automated assessment of the performance of: protein structure prediction methods (category 3D), ligand binding prediction methods (category LB) and model quality estimation methods (category QE). CAMEO is continuously maintained and developed (beta.cameo3d.org) and actually counts 57 different methods registered that are developed by 18 different groups.

Project Website

QMEAN - Quality Assessment of Protein Structures

The QMEAN server provides access to two scoring functions successfully tested at the eighth round of the community-wide blind test experiment CASP. The user can choose between the composite scoring function QMEAN, which derives a quality estimate on the basis of the geometrical analysis of single models, and the clustering-based scoring function QMEANclust which calculates a global and local quality estimate based on a weighted all-against-all comparison of the models from the ensemble provided by the user.

Project Website

PMP - Protein Model Portal

The Protein Model Portal (PMP) gives access to the various models that can be leveraged from PSI targets and other experimental protein structures by comparative modeling methods. The current release of the portal allows searching 13.5 million precomputed model structures provided by different partner sites, and provides access to various interactive services for template selection, target-template alignment, model building, and quality assessment.

Project Website

IPLT - Images Processing Library and Toolkit

The Image Processing Library & Toolbox is an open-source project, released under the GPL. It is primarily aimed at the electron microscopy community, with particular emphasis on 2D electron crystallography. It consists of several modular class libraries written in C++, each exposing a majority of their interface to Python, upon which the processing logic is build.

Project Website

lDDT - Local Distance Difference Test

The local Distance Difference Test (lDDT) is a superposition-free score which evaluates local distance differences in a model compared to a reference structure.

Project Website

Project Funding

Swiss Institute of Bioinformatics

Biozentrum, University of Basel