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
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
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.
Citation to related publication:
Title:
Genes of Danio rerio, zebrafish reconstructed with EvidentialGene
The evigene_beetle_tribolium2014 archive package contains a complete, reconstructed gene set of Tribolium castaneum, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Tribolium castaneum reconstructed with EvidentialGene
Click on the PURL link below in the "Link(s) to data and video for this item" section to download the dataset.
Citation to related publication:
Title:
Data for "Spatially variable increase in rock uplift in the northern U.S. Cordillera recorded in the distribution of river knickpoints and incision depths"
The evigene_tick_ixoscap2014 archive package contains a complete, reconstructed gene set of Ixodes scapularis, deer tick, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Ixodes scapularis, deer tick reconstructed with EvidentialGene
The evigene_cacao2013 archive package contains a complete, reconstructed gene set of Theobroma cacao, chocolate tree, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Theobroma cacao, chocolate tree reconstructed with EvidentialGene
The evigene_seaurchin_lytvar2017 archive package contains a complete, reconstructed gene set of Lytechinus variegatus, green sea urchin, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Lytechinus variegatus, green sea urchin reconstructed with EvidentialGene
The evigene_daphnia_pulex2010 archive package contains a complete, reconstructed gene set of Daphnia pulex, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Daphnia pulex reconstructed with EvidentialGene
The evigene_mosquito_aedes2016 archive package contains a complete, reconstructed gene set of Aedes aegypti, mosquito, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Aedes aegypti, mosquito reconstructed with EvidentialGene
The evigene_whitefly_bemitab2017 archive package contains a complete, reconstructed gene set of Bemisia tabaci, whitefly, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Bemisia tabaci, whitefly reconstructed with EvidentialGene
The evigene_tick_rhipic2014 archive package contains a complete, reconstructed gene set of Rhipicephalus pulchellus, zebra tick, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Rhipicephalus pulchellus, zebra tick reconstructed with EvidentialGene
The evigene_daphnia_galeata2016 archive package contains a complete, reconstructed gene set of Daphnia galeata, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Daphnia galeata reconstructed with EvidentialGene
The evigene_killifish2014 archive package contains a complete, reconstructed gene set of Fundulus heteroclitus, atlantic killifish, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Fundulus heteroclitus, atlantic killifish reconstructed with EvidentialGene
The evigene_pig2018 download contains a complete, reconstructed gene set of model animal Pig, Sus scrofa, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of the Pig, Sus scrofa, reconstructed with EvidentialGene
The evigene_mosquito_anoalb2016 archive package contains a complete, reconstructed gene set of Anopheles albimanus, mosquito, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Anopheles albimanus, mosquito reconstructed with EvidentialGene
The evigene_shrimp_penamon2013 archive package contains a complete, reconstructed gene set of Penaeus monodon, tiger shrimp, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Penaeus monodon, tiger shrimp reconstructed with EvidentialGene
The evigene_daphnia_magna2014 archive package contains a complete, reconstructed gene set of Daphnia magna, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Daphnia magna reconstructed with EvidentialGene
The evigene_daphnia_pulex2017 archive package contains a complete, reconstructed gene set of Daphnia pulex, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Daphnia pulex reconstructed with EvidentialGene
The evigene_mosquito_anofun2016 archive package contains a complete, reconstructed gene set of Anopheles funestus, mosquito, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
Citation to related publication:
Title:
Genes of Anopheles funestus, mosquito reconstructed with EvidentialGene
