BACKGROUND: Post-translational modifications (PTMs) constitute a major aspect of protein biology, particularly signaling events. Conversely, several different pathophysiological PTMs are hallmarks of oxidative imbalance or inflammatory states and are strongly associated with pathogenesis of autoimmune diseases or cancers. Accordingly, it is of interest to assess both the biological and structural effects of modification. For the latter, computer-based modeling offers an attractive option. We thus identified the need for easily applicable modeling options for PTMs. RESULTS: We developed PyTMs, a plugin implemented with the commonly used visualization software PyMOL. PyTMs enables users to introduce a set of common PTMs into protein/peptide models and can be used to address research questions related to PTMs. Ten types of modification are currently supported, including acetylation, carbamylation, citrullination, cysteine oxidation, malondialdehyde adducts, methionine oxidation, methylation, nitration, proline hydroxylation and phosphorylation. Furthermore, advanced settings integrate the pre-selection of surface-exposed atoms, define stereochemical alternatives and allow for basic structure optimization of the newly modified residues. CONCLUSION: PyTMs is a useful, user-friendly modelling plugin for PyMOL. Advantages of PyTMs include standardized generation of PTMs, rapid time-to-result and facilitated user control. Although modeling cannot substitute for conventional structure determination it constitutes a convenient tool that allows uncomplicated exploration of potential implications prior to experimental investments and basic explanation of experimental data. PyTMs is freely available as part of the PyMOL script repository project on GitHub and will further evolve. Graphical Abstract PyTMs is a useful PyMOL plugin for modeling common post-translational modifications.

For pt.I, see ibid., vol.41, no.3, p.502-208 (1993). Properties of a specific class of interpolators that are based upon polynomials are discussed. Several implementations are described, one of which is particularly convenient in practical hardware. Simulations demonstrate that simple interpolators give excellent performance. In many cases, two-point, linear interpolation is adequate. If better performance is needed, classical four-point, third-order polynomials could be used. Better yet, a novel four-point interpolating filter with piecewise-parabolic impulse response can have performance superior to that of the standard cubic interpolator and still be implemented much more simply. The NCO-based control method presented in Part I is shown to be equivalent to a conventional phase locked loop and its operation is verified by simulation.>

The limiting factor in the use of computer tools for the design of communications systems is often the amount of human intervention needed, rather than the actual computation time. A technique is presented by which a large proportion of the low-level decision making is delegated to the computer, thereby allowing the designer to concentrate on the engineering aspects and higher-level tradeoffs. The implementation described can be used with existing design programs (e.g., transmission simulators). The possibilities and limitations of the technique are discussed, and several examples of its application are given.>