FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations

Steinmann, Casper; Ibsen, Mikael W.; Hansen, Anne S.; Jensen, Jan H.

doi:10.1371/journal.pone.0044480

Cited by 41 publications

(45 citation statements)

References 33 publications

(36 reference statements)

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“…90 In all FMO/FDD calculations, STO-3G and 6-31G(d) were used for layers L 1 and L 2 , respectively, and the method is denoted by and the geometry was optimized with AMBER99 force field 91 using AMBER12. 92 In spectra simulations, the broadening parameter of 10 cm −1 is used for the line width.…”

Section: Computational Detailsmentioning

confidence: 99%

Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method

Nakata

Fedorov

Nagata

et al. 2015

J. Chem. Theory Comput.

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The fully analytic first and second derivatives of the energy in the frozen domain formulation of the fragment molecular orbital (FMO) were developed and applied to locate transition states and determine vibrational contributions to free energies. The development is focused on the frozen domain with dimers (FDD) model. The intrinsic reaction coordinate method was interfaced with FMO. Simulations of IR and Raman spectra were enabled using FMO/FDD by developing the calculation of intensities. The accuracy is evaluated for S(N)2 reactions in explicit solvent, and for the free binding energies of a protein-ligand complex of the Trp cage protein (PDB: 1L2Y ). FMO/FDD is applied to study the keto-enol tautomeric reaction of phosphoglycolohydroxamic acid and the triosephosphate isomerase (PDB: 7TIM ), and the role of amino acid residue fragments in the reaction is discussed.

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Section: Computational Detailsmentioning

confidence: 99%

Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method

Nakata

Fedorov

Nagata

et al. 2015

J. Chem. Theory Comput.

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“…[25] Each fragment consisted of two amino acid residues generated using FragIt program. [24] In the PIE calculations, the total energy E is decomposed into…”

Section: Methodsmentioning

confidence: 99%

Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method

Simoncini

Nakata

Ogata

et al. 2015

Molecular Informatics

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Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.

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“…FragIt [112] generates fragments of large molecules to use as input files in quantum chemistry programs that support fragment based methods.…”

Section: Quantum Chemistrymentioning

confidence: 99%

Open source molecular modeling

Pirhadi

Sunseri

2016

Journal of Molecular Graphics and Modelling

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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. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry.

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FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations

Cited by 41 publications

References 33 publications

Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method

Simulations of Chemical Reactions with the Frozen Domain Formulation of the Fragment Molecular Orbital Method

Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method

Open source molecular modeling

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