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- Smith, Daniel G. A., et al.
(author)
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Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine) : Automation and interoperability among computational chemistry programs
- 2021
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In: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 155:20
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Journal article (peer-reviewed)abstract
- Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.
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2. |
- Zhu, Lijuan, et al.
(author)
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Binding modes of cabazitaxel with the different human beta-tubulin isotypes : DFT and MD studies
- 2020
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In: Journal of Molecular Modeling. - : Springer Science and Business Media LLC. - 1610-2940 .- 0948-5023. ; 26:6
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Journal article (peer-reviewed)abstract
- Taxanes (paclitaxel, docetaxel, cabazitaxel) are anticancer drugs as microtubule inhibitors. Following our previous studies on paclitaxel and docetaxel, in this work, we examine cabazitaxel and compare these three taxenes. The binding interaction of three taxanes with various beta-tubulin isotypes is studied by homology modeling, molecular docking, and molecular dynamics simulations. The results show that the effects of docetaxel on beta I-tubulin (- 29.5 kcal/mol) and of paclitaxel on beta IIa-tubulin (- 25.5 kcal/mol) are much stronger than their effects on beta III-tubulin (- 17.8 kcal/mol and - 8.6 kcal/mol, respectively). However, the effect of cabazitaxel on beta III-tubulin (- 23.0 kcal/mol) is comparable with that on beta I-tubulin (- 24.0 kcal/mol) and beta IIa-tubulin (- 25.9 kcal/mol), consistent with the fact that overexpression of beta III-tubulin increases the drug resistance to paclitaxel and docetaxel, but has little influence for cabazitaxel. This theoretical research supports the use of cabazitaxel for patients who are resistant to the action of paclitaxel and docetaxel.
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