@proceedings {Kmiecik2008a, title = {Designing an Automatic Pipeline for Protein Structure Prediction Designing an Automatic Pipeline for Protein Structure Prediction}, journal = {From Computational Biophysics to Systems Biology (CBSB08)}, volume = {40}, year = {2008}, pages = {105{\textendash}108}, 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{\textquoteright}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{\textquoteright}t guarantee the highest possible performance. Therefore, human intervention is made possible at every stage of modeling.}, isbn = {9783981084368}, author = {Sebastian Kmiecik and Michal Jamroz and Anna Zwolinska and Pawel Gniewek and Andrzej Koli{\'n}ski and Ulrich H. E. Hansmann and Jan H. Meinke and Sandipan Mohanty and Walter Nadler and Olav Zimmermann} }