MS42-P02 Expanding partial structures by assembling most probable side chain compositionKnowledge of biological structures and their interaction plays an essential role in the comprehension of biological mechanisms. Crystallography and recently CryoEM provide macromolecular models in atomic detail. CryoEM requires the interpretaion of a map of heterogeneous resolution, while crystallography requires to overcome the bottleneck of phasing. Phasing through multisolution placement of ubiquitous small fragments, such as alpha-helices and beta-strands, with PHASER  followed by density modification and tracing with SHELXE is now established as an effective method to solve the phase problem, provided the structure is not too large and data to high resolution are available . When the resolution limit of the diffraction data does not reach 2 Å, and if the helical content is low, fragments may still be correctly placed, but density modification and autotracing often fails to reveal the rest of the structure. The process stalls as no additional features develop in the map, whether in the extension of the polypeptide chain or in side chain electron density. SEQUENCE SLIDER is being developed to extend the initial and intermediate partial models by assembling multiple models from the most probable side chains into the current fragments. As secondary structure prediction of residues from sequence is reliable, this information is used to restrict possibilities matching the secondary structure of residues of the partial model and traces. Moreover, additional filters are applied based on free energy calculation using crystal contacts and assignment of hydrophobic and hydrophilic residues to protein cores and surface, respectively. Models with different side chain assignment are assembled with SCWRL4  and may be modified with refinement. Extended partial structures with the best indicators are pushed on to density modification and tracing with SHELXE. Specific strategies of SLIDER have been designed within ARCIMBOLDO_SHREDDER and in the coil coiled mode. Three novel structures and other test cases determined with SLIDER are presented.References:
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