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- Q6675846 subject Q7217021.
- Q6675846 subject Q8799442.
- Q6675846 subject Q8802913.
- Q6675846 abstract "Template:OutdatedLoop modeling is a problem in protein structure prediction requiring the prediction of the conformations of loop regions in proteins with or without the use of a structural template. Computer programs that solve these problems have been used to research a broad range of scientific topics from ADP to breast cancer. Because protein function is determined by its shape and the physiochemical properties of its exposed surface, it is important to create an accurate model for protein/ligand interaction studies. The problem arises often in homology modeling, where the tertiary structure of an amino acid sequence is predicted based on a sequence alignment to a template, or a second sequence whose structure is known. Because loops have highly variable sequences even within a given structural motif or protein fold, they often correspond to unaligned regions in sequence alignments; they also tend to be located at the solvent-exposed surface of globular proteins and thus are more conformationally flexible. Consequently, they often cannot be modeled using standard homology modeling techniques. More constrained versions of loop modeling are also used in the data fitting stages of solving a protein structure by X-ray crystallography, because loops can correspond to regions of low electron density and are therefore difficult to resolve.Regions of a structural model that are predicted by non-template-based loop modeling tend to be much less accurate than regions that are predicted using template-based techniques. The extent of the inaccuracy increases with the number of amino acids in the loop. The loop amino acids' side chains dihedral angles are often approximated from a rotamer library, but can worsen the inaccuracy of side chain packing in the overall model. Andrej Sali's homology modeling suite MODELLER includes a facility explicitly designed for loop modeling by a satisfaction of spatial restraints method. All methods require an upload of the PDB file and some require the specification of the loop location.".
- Q6675846 wikiPageExternalLink superlooper.
- Q6675846 wikiPageExternalLink falc-loop.seoklab.org.
- Q6675846 wikiPageExternalLink modloop.
- Q6675846 wikiPageExternalLink ~rapper.
- Q6675846 wikiPageWikiLink Q1128023.
- Q6675846 wikiPageWikiLink Q128581.
- Q6675846 wikiPageWikiLink Q146505.
- Q6675846 wikiPageWikiLink Q15712714.
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- Q6675846 wikiPageWikiLink Q290042.
- Q6675846 wikiPageWikiLink Q3273544.
- Q6675846 wikiPageWikiLink Q3859815.
- Q6675846 wikiPageWikiLink Q425105.
- Q6675846 wikiPageWikiLink Q4756078.
- Q6675846 wikiPageWikiLink Q4995178.
- Q6675846 wikiPageWikiLink Q5244958.
- Q6675846 wikiPageWikiLink Q5767913.
- Q6675846 wikiPageWikiLink Q579211.
- Q6675846 wikiPageWikiLink Q7217021.
- Q6675846 wikiPageWikiLink Q7251429.
- Q6675846 wikiPageWikiLink Q8054.
- Q6675846 wikiPageWikiLink Q8066.
- Q6675846 wikiPageWikiLink Q826582.
- Q6675846 wikiPageWikiLink Q827246.
- Q6675846 wikiPageWikiLink Q847556.
- Q6675846 wikiPageWikiLink Q864267.
- Q6675846 wikiPageWikiLink Q8799442.
- Q6675846 wikiPageWikiLink Q8802913.
- Q6675846 wikiPageWikiLink Q899656.
- Q6675846 wikiPageWikiLink Q899689.
- Q6675846 wikiPageWikiLink Q901969.
- Q6675846 wikiPageWikiLink Q905186.
- Q6675846 wikiPageWikiLink Q911907.
- Q6675846 comment "Template:OutdatedLoop modeling is a problem in protein structure prediction requiring the prediction of the conformations of loop regions in proteins with or without the use of a structural template. Computer programs that solve these problems have been used to research a broad range of scientific topics from ADP to breast cancer.".
- Q6675846 label "Loop modeling".