User:Eric Martz/Introduction to Structural Bioinformatics I: Difference between revisions
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:<span style="font-size:130%">2. Structure Knowledge.</span> | :<span style="font-size:130%">2. Backbone Representation.</span> | ||
::A. [http://www.umass.edu/molvis/tutorials/hemoglobin/pepstruc.htm Peptides and Backbones] (within a tutorial on hemoglobin) | |||
::B. [http://firstglance.jmol.org/fg.htm?mol=1pgb Small Protein in FirstGlance] (use Vines, Cartoon) | |||
:<span style="font-size:130%">3. Structure Knowledge.</span> | |||
::A. Although sequence specifies fold, scientists '''cannot yet predict the fold from the sequence'''. Therefore, fold must be determined by empirical (experimental) methods. The most common methods for determining the 3D structure of a protein molecule are: | ::A. Although sequence specifies fold, scientists '''cannot yet predict the fold from the sequence'''. Therefore, fold must be determined by empirical (experimental) methods. The most common methods for determining the 3D structure of a protein molecule are: | ||
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::E. Crystallographers publish the [[asymmetric unit]] of the crystal. It may be identical with the [[biological unit]] (the functional form of the molecule), or it may be only part of the biological unit, or it may contain multiple copies of the biological unit. See [[Biological unit#Examples|examples]]. | ::E. Crystallographers publish the [[asymmetric unit]] of the crystal. It may be identical with the [[biological unit]] (the functional form of the molecule), or it may be only part of the biological unit, or it may contain multiple copies of the biological unit. See [[Biological unit#Examples|examples]]. | ||
:::Interchain contacts that occur in the asymmetric unit that are absent in the biological unit are an artifact of crystallization, termed [[crystal contacts]]. | :::Interchain contacts that occur in the asymmetric unit that are absent in the biological unit are an artifact of crystallization, termed [[crystal contacts]]. | ||
==III. Choose a Molecule to Explore== | ==III. Choose a Molecule to Explore== | ||
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:B. The abstract of the publication about this structure, which usually mentions the '''function of the molecule''' if known. | :B. The abstract of the publication about this structure, which usually mentions the '''function of the molecule''' if known. | ||
:C. The '''number of polymer chains''' under ''About this Structure''. | :C. The '''number of polymer chains''' under ''About this Structure''. | ||
:D. Full '''names of ligands and non-standard residues''' (displayed when their green links are clicked beneath the molecule). Example: [[2src]]. | :D. Full '''names of ligands and non-standard residues''' (displayed when their '''<font color="#00c000">green links</font>''' are clicked beneath the molecule). Example: [[2src]]. | ||
:E. Evolutionary conservation. | :E. Evolutionary conservation. | ||
::See [[Introduction to Evolutionary Conservation]]. | ::See [[Introduction to Evolutionary Conservation]]. | ||
