NMR‐Guided Molecular Docking of a Protein–Peptide Complex Based on Ant Colony Optimization

Standard docking approaches used for the prediction of protein–ligand complexes in the drug development process have problems identifying the correct binding mode of large flexible ligands. Herein we show how additional experimental data from NMR experiments can be used to predict the binding mode of a mucin 1 (MUC‐1) pentapeptide recognized by the breast‐cancer‐selective monoclonal antibody SM3. Distance constraints derived from trNOE and saturation transfer difference NMR experiments are combined with the docking approach PLANTS. The resulting complex structures show excellent agreement with the NMR data and with a published X‐ray crystal structure. The method was then further tested on two complexes in order to demonstrate its more general applicability: T‐antigen disaccharide bound to Maclura pomifera agglutinin, and the inhibitor SBi279 bound to S100B protein. Our new approach has the advantages of being fully automatic, rapid, and unbiased; moreover, it is based on relatively easily obtainable experimental data and can greatly increase the reliability of the generated structures.     

Look-ahead on pushdowns

The general notion of look-ahead on pushdowns is used to prove that (1) the deterministic iterated pushdown languages are closed under complementation, (2) the deterministic iterated pushdown languages are properly included in the non-deterministic iterated pushdown languages; the counter example is a very simple linear context-free language, independent of the amount of iteration, (3) LL(k) iterated indexed grammars can be parsed by deterministic iterated pushdown automata, and (4) it is decidable whether an iterated indexed grammar is LL(k). Analogous results hold for iterated pushdown automata with regular look-ahead on the input, and LL-regular iterated indexed grammars.     

Measurements of Si ion stopping in amorphous silicon

The stopping of ²⁸Si ions in polycrystalline Si foils has been measured over the energy range 0.1–3.3 MeV per nucleon. For the low energy interval (0.1–0.5 MeV per nucleon), time of flight-energy elastic recoil detection analysis method was used, whilst for the high energy region (1.2–3.3 MeV per nucleon) the energy loss in the same foil was measured using a Si p–i–n diode with the ²⁸Si ions directly incident on the foil following acceleration. Below the stopping maximum the results are in good agreement with literature data based on Doppler shift measurements of short nuclear lifetimes but are about 20% smaller than the SRIM prediction. Above the stopping maximum the data are in agreement with SRIM within the limits of statistical uncertainty.     

Aero‐hygrothermisches Verhalten von Umfassungskonstruktionen mit Hohlräumen

Aero‐hygro‐thermal behaviour of building enslosure components with opened and enclosed air cavities. Air cavities with different functions can be found in historical as well as in modern structural design. In the past, air cavities mainly have been made for practical reasons to improve the thermal insulation properties of wall and roof constructions. In modern architecture, hollow spaces frequently arise due to constructional or due to aesthetic reasons such as in glass curtain walls or in cladding of inside walls. On environmental grounds the obligations towards the energy efficient construction and operating of buildings are tightened increasingly. This leads, under compliance with today's room climatic requirements, to the focusing of activities on appropriate use of building materials and the expenses and energy optimized design of building envelopes. On the rehabilitation of historical structures often questions regarding the hygro‐thermal evaluation of such air cavities and the therein occurring convection processes arise. So, a long term cross flow in open cavities with moisture‐loaded air can cause damages on the service ability and bearing capacity of components. The consideration of cross flows in enclosed cavities of single components or in open constructions, such as wall or roof constructions, can be calculated at present only by use of special assumptions. For the solution of this complex problem the coupling of a CFD‐solver with a hygro‐thermal building simulation software has been carried out. Within the scope of a research project a CaFD (cavity fluid dynamics) simulation code has been developed which especially is adjusted to the requirements and boundary conditions of hygro‐thermal component simulations. Therefore, the functional range concentrates on building physical problems definitions of structural designs. With the implementation of the CaFD‐tool as an additional application for the software package DELPHIN 4.x, an independent operational CFD software module has been developed. By means of the SIMPLE‐Algorithm it solves the Navier‐Stokes‐Equations additionally under consideration of the heat and mass transport in the cavity. A data interface controls the interactive data interchange between DELPHIN and the CaFD‐tool. The presentation of simulations of the aero‐hygro‐thermal behaviour of components with opened and enclosed air cavities completes the contribution. With selected test cases the coupled simulation is analysed and discussed more closely from the building physical point of view.