Twilight reloaded: the peptide experience
نویسندگان
چکیده
The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein-peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided.
منابع مشابه
Painless Childbirth
on in France. The book represents a lay agitation for " twilight sleep," and describes the experiences of several women who have been delivered at Freiburg. From the obstetrical point of view, the principal interest lies in the three appendices where Kronig and Gauss give the details of the method and meet the various arguments which have been launched against " twilight sleep." The writers evi...
متن کاملAtmospheric ozone and colors of the Antarctic twilight sky.
Zenith skylight is often distinctly blue during clear civil twilights, and much of this color is due to preferential absorption at longer wavelengths by ozone's Chappuis bands. Because stratospheric ozone is greatly depleted in the austral spring, such decreases could plausibly make Antarctic twilight colors less blue then, including at the zenith. So for several months in 2005, we took digital...
متن کاملTwilight spectral dynamics and the coral reef invertebrate spawning response.
There are dramatic and physiologically relevant changes in both skylight color and intensity during evening twilight as the pathlength of direct sunlight through the atmosphere increases, ozone increasingly absorbs long wavelengths and skylight becomes increasingly blue shifted. The moon is above the horizon at sunset during the waxing phase of the lunar cycle, on the horizon at sunset on the n...
متن کاملThe Matrix Reloaded: New Insights from Type IV Collagen Derived Endogenous Angiogenesis Inhibitors and their Mechanism of Action
Angiogenesis, the process of neovascularization from parent blood vessels, is a prerequisite for many physiological and pathological conditions that is regulated by a balance between the levels of endogenous angiogenic stimulators and matrix reloaded angiogenic regulators. Several non-collagenous carboxy terminal end domains in chains of type IV collagen matrix reloaded molecules selectively in...
متن کامل