lecture9 - Bioinformatics 2: Lecture 9 • Fixing errors....

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Unformatted text preview: Bioinformatics 2: Lecture 9 • Fixing errors. Modeling errors* • Backbone errors – indel in helix – indel in strand – loose loops – missing H-bonds • Sidechain errors – buried charges, polar sidechains – too many exposed hydrophobics – phi > 0 and not Gly, Asn – (phi < -90 or phi > 0 ) and Pro • Voids *Omitting obvious errors: collisions, stretched bonds, distorted planar groups... realign realign realign realign or minimize realign, MD realign realign or minimize MD, rotamer search, minimize restrain, minimize Modeling errors* • Backbone errors – indel in helix – indel in strand – loose loops – missing H-bonds • Sidechain errors – buried charges, polar sidechains – too many exposed hydrophobics – phi > 0 and not Gly, Asn – (phi < -90 or phi > 0 ) and Pro • Voids *Omitting obvious errors: collisions, stretched bonds, distorted planar groups... realign realign realign realign or minimize realign, MD realign realign or minimize MD, rotamer search, minimize restrain, minimize An exception to the no-insertions-in-strand...
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lecture9 - Bioinformatics 2: Lecture 9 • Fixing errors....

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