TY - Generic T1 - Designing an Automatic Pipeline for Protein Structure Prediction Designing an Automatic Pipeline for Protein Structure Prediction T2 - From Computational Biophysics to Systems Biology (CBSB08) Y1 - 2008 A1 - Sebastian Kmiecik A1 - Michal Jamroz A1 - Anna Zwolinska A1 - Pawel Gniewek A1 - Andrzej Koliński A1 - Ulrich H. E. Hansmann A1 - Jan H. Meinke A1 - Sandipan Mohanty A1 - Walter Nadler A1 - Olav Zimmermann AB - 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. JF - From Computational Biophysics to Systems Biology (CBSB08) VL - 40 SN - 9783981084368 ER -