JACOB: An enterprise framework for computational chemistry

Waller, Mark P.; Dresselhaus, Thomas

doi:10.1002/jcc.23272

Cited by 11 publications

(4 citation statements)

References 20 publications

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“…Computational chemistry has been gaining space and increasing recognition within research centers. This fact is due to the development of new computers with greater processing power and consequently the creation of new methods that make the results obtained through computational computations increasingly consistent with those obtained experimentally 258 v.5 n.1 2019 (WALLER et al, 2013;ALLOUCHE et. al., 2011).…”

Section: Introductionmentioning

confidence: 76%

Computational Study of Organic Compounds – An Application for Learning in Chemistry

et al. 2019

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Organic chemistry is a theme not so easy to understand by undergraduating students. The motivation of this work was carried out computational study of three different molecules by molecular modeling using classic and semi-empirical methods besides open-source softwares. The optimized structures were visualized through 3D representations which made the study more understanding. Physical chemistry properties were extracted from all molecules. For the molecule one there was good correlation between the calculation methods. For the molecule two and more complex structures like molecule three and four there was possible influence of steric effect showing that each method is applicable for each study system.

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Section: Introductionmentioning

confidence: 76%

Computational Study of Organic Compounds – An Application for Learning in Chemistry

et al. 2019

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“…The HMO searches were performed using JACOB, which is our own framework for computational chemistry, based on enterprise software design practices. The PM6-DH+ semiempirical gas-phase single-point energies were computed using MOPAC2012 .…”

Section: Methodsmentioning

confidence: 99%

Hybrid Metaheuristic Approach for Nonlocal Optimization of Molecular Systems

Dresselhaus

Kumbhar

Waller

2013

J. Chem. Theory Comput.

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Accurate modeling of molecular systems requires a good knowledge of the structure; therefore, conformation searching/optimization is a routine necessity in computational chemistry. Here we present a hybrid metaheuristic optimization (HMO) algorithm, which combines ant colony optimization (ACO) and particle swarm optimization (PSO) for the optimization of molecular systems. The HMO implementation meta-optimizes the parameters of the ACO algorithm on-the-fly by the coupled PSO algorithm. The ACO parameters were optimized on a set of small difluorinated polyenes where the parameters exhibited small variance as the size of the molecule increased. The HMO algorithm was validated by searching for the closed form of around 100 molecular balances. Compared to the gradient-based optimized molecular balance structures, the HMO algorithm was able to find low-energy conformations with a 87% success rate. Finally, the computational effort for generating low-energy conformation(s) for the phenylalanyl-glycyl-glycine tripeptide was approximately 60 CPU hours with the ACO algorithm, in comparison to 4 CPU years required for an exhaustive brute-force calculation.

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“…The conformation of the side chain of the Arg74 residue in all further steps of the modeling procedure was taken from the crystal structure. The lowest energy structure obtained from each of the 20 runs of the conformational search proce-dure 35,36 was further optimized at the same level of theory using the EigenFollowing (EF) [37][38][39] optimizer in MOPAC2009. 34 All of the gas-phase linker structures were found to be within an energy range of 10.36 kcal mol 21 for the natural linker and in the range of 2.84 kcal mol 21 for the synthetic linker.…”

Section: Computational Detailsmentioning

confidence: 99%

Naturally and synthetically linked lys48 diubiquitin: a QM/MM study

Dresselhaus

Weikart²,

Mootz³

et al. 2013

RSC Adv.

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Site-specific chemical conjugates of proteins with ubiquitin-like modifiers are a powerful tool for biochemists to probe the function of these post-translational modifications. As a prominent example, the seven native isopeptide-linked diubiquitins serve as models to study polyubiquitin chains, but not all of them can be prepared by enzymatic means. To date, several approaches to access synthetically conjugated diubiquitins have been reported, however, an experimental structure of such a molecule with an unnatural linker remains elusive. Therefore, here we present structural models of the Lys48-connected diubiquitin with the natural isopeptide and a synthetic triazole linker using hybrid quantum mechanical and molecular mechanical (QM/MM) methods. Despite differences in the flexibility of the linkers, the systems with the synthetic and natural linker were found to be very similar in regard to the analyzed geometric features. This provides computational support for the use of the synthetically linked conjugate as a mimic of the natural isopeptide bonded diubiquitin.

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JACOB: An enterprise framework for computational chemistry

Cited by 11 publications

References 20 publications

Computational Study of Organic Compounds – An Application for Learning in Chemistry

Computational Study of Organic Compounds – An Application for Learning in Chemistry

Hybrid Metaheuristic Approach for Nonlocal Optimization of Molecular Systems

Naturally and synthetically linked lys48 diubiquitin: a QM/MM study

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