Abstract
Within BioExcel, the European Center of Excellence (CoE) for Computational Biomolecular research, we developed new web services for the modelisation of biomolecular complexes powered by EGI HTC resources distributed worldwide.
Pioneer in the field of integrative modelling, HADDOCK (haddock.science.uu.nl) is an information-driven modelling service for the prediction of the three-dimensional structure of biomolecular assemblies. More than 7,700 users worldwide make use of HADDOCK’s user-friendly web interface. As of September 2016, more than 130,000 user submissions have been processed by the server, which translates into more than 8 million jobs a year. The HADDOCK support center is powered by a dedicated BioExcel forum (http://ask.bioexcel.eu).
DisVis (http://milou.science.uu.nl/services/DISVIS) allows you to visualizes and quantify the information content of distance restraints between macromolecular complexes. It performs a full and systematic 6-dimensional search of the three translational and rotational degrees of freedom to determine the number of complexes consistent with the restraints. In addition, it outputs the percentage of restraints being violated and a density that represents the center-of-mass position of the scanning chain corresponding to the highest number of consistent restraints at every position in space.
PowerFit (http://milou.science.uu.nl/services/POWERFIT) automatically fits high-resolution atomic structures in cryo-EM densities. To this end it performs a full-exhaustive 6-dimensional cross-correlation search between the atomic structure and the density. It takes as input an atomic structure in PDB-format and a cryo-EM density with its resolution; and outputs positions and rotations of the atomic structure corresponding to high correlation values. PowerFit uses the local cross-correlation function as its base score, enhanced by a Laplace pre-filter and/or core-weighting to minimize overlapping densities from neighboring subunits.
Pioneer in the field of integrative modelling, HADDOCK (haddock.science.uu.nl) is an information-driven modelling service for the prediction of the three-dimensional structure of biomolecular assemblies. More than 7,700 users worldwide make use of HADDOCK’s user-friendly web interface. As of September 2016, more than 130,000 user submissions have been processed by the server, which translates into more than 8 million jobs a year. The HADDOCK support center is powered by a dedicated BioExcel forum (http://ask.bioexcel.eu).
DisVis (http://milou.science.uu.nl/services/DISVIS) allows you to visualizes and quantify the information content of distance restraints between macromolecular complexes. It performs a full and systematic 6-dimensional search of the three translational and rotational degrees of freedom to determine the number of complexes consistent with the restraints. In addition, it outputs the percentage of restraints being violated and a density that represents the center-of-mass position of the scanning chain corresponding to the highest number of consistent restraints at every position in space.
PowerFit (http://milou.science.uu.nl/services/POWERFIT) automatically fits high-resolution atomic structures in cryo-EM densities. To this end it performs a full-exhaustive 6-dimensional cross-correlation search between the atomic structure and the density. It takes as input an atomic structure in PDB-format and a cryo-EM density with its resolution; and outputs positions and rotations of the atomic structure corresponding to high correlation values. PowerFit uses the local cross-correlation function as its base score, enhanced by a Laplace pre-filter and/or core-weighting to minimize overlapping densities from neighboring subunits.
| Original language | English |
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| Publication status | Published - 2016 |