Download the software applications and data used for the 2017 Student Cluster Competition by clicking the URLs below: Model for Prediction Across Scales (MPAS); Born seismic imaging tool; MrBayes program for Bayesian inference and model choice; LAMMPS molecular dynamics (MD) code. Note that download times may vary.
To gain insight into how the POP scaffold might give rise to the observed ArM selectivity, molecular dynamics simulations were conducted on models of 5-G that involved different starting coordination states of dirhodium cofactor 1. Three starting coordination states (5-G apo, 5-G with parameterized Rh-His bond, 5-G without Rh-His bond) were studied. The initial structure of 5-G apo was constructed from the crystal structure of POP, with the following amino acids mutations made using VMD17: S477F/E104A/F146A/K199A/D202A/S301G/G99S/Y326H/Q98P/S99H/V71G/E283G. The 5-G with Rh-His and 5-G without Rh-His bond models were constructed by mutating S477Z (Z is azidophenylalanine, where dirhodium cofactor 1 covalently links to the protein), which is the only other mutation from 5-G apo. No other changes where made to the model without a Rh-His bond. The Rh-His model contains a parameterized H326 bond to one of the dirhodium atoms, as shown in Figure 2D. MD simulations were performed for the 5-G apo, with Rh-His and no Rh-His POP enzymes. All three structures were bathed in a 0.15M KCl solution using the Solution Builder Module in CHARMM-GUI.18 These systems were roughly 100 3/2 100 3/2 100 Å3 in dimension and contained ~ 110,000 atoms. The periodic boundary conditions were counted using the particle-mesh Ewald method with an automatic generated grid size. Once the simulation systems were generated, they were subjected to equilibration at 358.15 K. The system was first equilibrated in an NVT ensemble for 10 ns. The equilibration simulations were performed using NAMD2.14 GPU acceleration version package19 on Nvidia’s P100 GPUs. After equilibration, the systems were simulated for 1000 ns each in an NPT ensemble with temperature set to 358.15 K and the isotropic pressure set to 1 atm. Langevin thermostats with a damping coefficient of 1 ps-1 were used to keep the temperature constant. The cutoff of the van der Waals interactions and short-range electrostatic interactions were set to ~25 Å as suggested by the guesser script. The additive C36 force field was used in all the simulations performed here.20,21,22,23 The force field parameters for the covalently linked dirhodium cofactor 1 were generated using the GAAMP server.24
Supporting datasets for drill-down topic modeling workflow described in "Multi-level computational methods for interdisciplinary research in the HathiTrust Digital Library." PLOS ONE. https://doi.org/10.1371/journal.pone.0184188
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Supporting Data for "Multi-level computational methods for interdisciplinary research in the HathiTrust Digital Library"
The evigene_corn2016 archive package contains a complete, reconstructed gene set of Zea mays, corn plant, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Zea mays, corn plant reconstructed with EvidentialGene
The evigene_wasp_nasvit2012 archive package contains a complete, reconstructed gene set of Nasonia vitripennis, jewel wasp, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Nasonia vitripennis, jewel wasp reconstructed with EvidentialGene
The evigene_catfish2013 archive package contains a complete, reconstructed gene set of Ictalurus punctatus, catfish, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Ictalurus punctatus, catfish reconstructed with EvidentialGene
The evigene_locust_locumig2013 archive package contains a complete, reconstructed gene set of Locusta migratoria migratoria, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Locusta migratoria migratoria reconstructed with EvidentialGene
The evigene_honeybee_apismel2014 archive package contains a complete, reconstructed gene set of Apis mellifera, honey bee, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Apis mellifera, honey bee reconstructed with EvidentialGene
The evigene_shrimp_litova2013 archive package contains a complete, reconstructed gene set of Litopenaeus vannamei, white shrimp, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Litopenaeus vannamei, white shrimp reconstructed with EvidentialGene
The evigene_aphid_acypi2011 archive package contains a complete, reconstructed gene set of Acyrthosiphon pisum, pea aphid, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Acyrthosiphon pisum, pea aphid reconstructed with EvidentialGene
The evigene_daphnia_similoides2017 archive package contains a complete, reconstructed gene set of Daphnia similoides, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Daphnia similoides reconstructed with EvidentialGene
The evigene_arabidopsis2017 archive package contains a complete, reconstructed gene set of Arabidopsis thaliana, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Arabidopsis thaliana reconstructed with EvidentialGene
The evigene_beetle_pogocha2013 archive package contains a complete, reconstructed gene set of Pogonus chalceus, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Pogonus chalceus reconstructed with EvidentialGene
The evigene_pinetree2013 archive package contains a complete, reconstructed gene set of Pinus taeda, loblolly pine tree, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents. Click on the PURL link below in the "External Files" section to download the dataset.
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Genes of Pinus taeda, loblolly pine tree reconstructed with EvidentialGene
The evigene_zebrafish2017 archive package contains a complete, reconstructed gene set of Danio rerio, zebrafish, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Danio rerio, zebrafish reconstructed with EvidentialGene
