The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable....
MMTK (Molecular Modelling Toolkit) is a library written in Python (with some time critical parts written in C) for constructing and simulating molecular systems. Its capabilities include molecular dynamics, energy minimization, and normal mode analysis and it is well-suited for methods development. ...
MS is an integrated software for modelling and simulation. Its most important feature is the visual modelling environment, which facilitates researchers to better design and study various types of materials, such as ceramics, metals, polymers, composites, etc. [56]. Therefore, MS is often ...
If a 3D structure of a protein–carbohydrate complex is available (e.g. an X-ray structure), MD simulations can be performed to study the local interactions (hydrogen bonding, hydrophobic interactions, water bridges) in more detail [245,246] or to calculate free energy [247–249] and entrop...
converting wild-type alleles into drive alleles in the germline of drive heterozygotes. Here the authors demonstrate a genetic pest suppression system based on dominant female-sterile doublesex alleles and show that releases of transgenic males eliminated Drosophila cage populations, with modelling showing...
Chemical structures were extracted from literature and inputted to the modelling software (Molecular Operating Environment, MOE, v.2019.08, Chemical Computing Group, Montreal, QC, Canada) using the canonical SMILES codes from PubChem. If not available, the chemical structure was drawn manually using ...
withQiandQjthe corresponding charges andε0the permittivity of free space. In general, charges are assigned empirically to reproduce experimental observables such as known multipole moments or thermodynamic properties. The second stage in Box 1 represents the main computational loop of a molecular dyna...
spatial patterns with an associated algorithm. The tomography-based approach offers a convenient and imaging-free technique for exploring spatial genomics. Nonetheless, this method is often characterized by its comparatively lower resolution in comparison to imaging-based approaches. Additionally, it may ...
Modelling H2H2O in a similar environment and taking rotational energy levels from the 𝜈2=0,1ν2=0,1 and 𝜈3=0,1,2ν3=0,1,2 vibrational levels into account up to energies of 5000 cm−1−1 (as calculated by Faure et al. [24]) quickly brings the number of levels considered...
Modelling nucleophilic substitution at silicon in solution using hypervalent silicon compounds based on 2-thiopyridones. J. Chem. Soc. Perkin Trans. 2000, 2, 1059–1066. [Google Scholar] [CrossRef] Cordero, B.; Gómez, V.; Platero-Prats, A.E.; Revés, M.; Echeverría, J.; Cremades, ...