Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions

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Designing an Automatic Pipeline for Protein Structure Prediction Designing an Automatic Pipeline for Protein Structure Prediction

Source:

From Computational Biophysics to Systems Biology (CBSB08), Ulrich H. E. Hansmann, Jan H. Meinke, Sandipan Mohanty, Walter Nadler, Olav Zimmermann, Eds, 40:105–108, 2008

Abstract

Building accurate 3D structural models of proteins and protein assemblies is a challenging task. Our modeling technology is based on the CABS model, extensively tested, state-of-theart approach to protein structure prediction. The modeling process is divided into two stages: CABS fold assembly followed by the model refinement/selection procedure, using an all-atom representation and a more exact interaction scheme enabling high resolution structure prediction. Fold assembly can be done in a framework of a standard comparative modeling procedure, where spatial restraints are derived from alternative sequence alignments with a template/ templates. Preferentially in more difficult modeling cases, a new approach to comparative modeling can be used, which does not require the prior alignment. Selvita’s goal is to provide an integrated tool-kit for automated protein structure predictions. However, like blind prediction experiments show, due to high complexity of prediction tasks, fully automated approach often doesn’t guarantee the highest possible performance. Therefore, human intervention is made possible at every stage of modeling.