181 Works

Data for ‘Seismic evidence for partial melt below tectonic plates’ by Debayle et al., (2020)

European part of the Collaborative Seismic Earth Model (CSEM)

Teleseismic S-wave velocity model of the western US

Cultural Life: Figure 3 A,B

Dan C. BACIU

Dataset for numerical modeling to investigate conditions leading to single- or multi-slab plume-induced subduction initiation

Marzieh Baes, Stephan Sobolev, Taras Gerya & Sascha Brune
The data are the numerical modeling results to investigate plume-induced subduction initation on which the figures of the paper "Plume-induced subduction initiation: single- or multi-slab subduction?" by Baes, Sobolev, Gerya and Brune are based. Detailed description on how they are obtained is given in that article (Baes et al., 2020). The naming of the files is based on the number of figures in the paper. Each zipped file contains input files (init.t3c and mode.t3c) and...

Model of the Rabies virus L protein

A homology-based model of the RABV L protein was generated based on the structure of the vesicular stomatitis virus (VSV) L protein (PDB id: 5A22).

Model of the Rabies virus L terminal de novo initiation complex

A homology-based model of the RABV L terminal de novo initiation complex was generated based on the vesicular stomatitis virus (VSV) L terminal de novo initiation complex (Molecular Archive id: ma-5k432).

Mouse Eugenol Odorant Receptor

Molecular interactions of odorants with their olfactory receptors (ORs) are of central importance for the ability of the mammalian olfactory system to detect and discriminate a vast variety of odors with a limited set of receptors. How a particular OR binds and distinguishes different odorant molecules remains largely unknown on a structural basis. Here we investigated this question for the mouse eugenol receptor (mOR-EG). By screening a large odorant library, we discovered a wide range...

Bacillus subtilis YqjX protein

The YolD family (that includes both Bacillus subtilis YolD and YqjX (this model)) is part of the WYL-like superfamily, predicted to have an SH3 β-barrel fold related to Sm domains. In our analysis, among the closest detected structural matches were E. coli YaeO, a Rho-specific inhibitor of transcription termination, and a cyanobacterial Hfq homolog. Model assessment showed that YqjX and YolD sequences are indeed compatible with the SH3 β-barrel structure. Interestingly, UmuD' has an all...

Multidrug transporter AcrD of E. coli

Resistance-Nodulation-cell Division (RND) transporters AcrB and AcrD of Escherichia coli expel a wide range of substrates out of the cell in conjunction with AcrA and TolC, contributing to the onset of bacterial multidrug resistance. AcrB is the best characterized RND transporter, and its structure has been solved by several labs both without and with bound substrates and inhibitors. AcrD, a close homolog of AcrB, shares an overall sequence identity of nearly 66% (similarity ~80%) but...

Daisy simulation of Tofteng et al. 2002 column experiment with one artificial biopore

Maja Holbak & Efstathios Diamantopoulos

CYP21A2Bruque2016

A model of the human CYP21A2 protein based on the structure of the bovine CYP21A2 (PDB ID: 3QZ1) was generated using MODELLER version 9.11 including heme cofactor explicitly. Amino acid sequence was taken from UniProt (NP_000491.4) while alignments were performed with MEGA 4 software. A significant improvement of the model was obtained by manually displacing L129 in the automatic alignment and iterative loop refinement. The use of multiple templates of other proteins of the CYP...

Mosquée de Marcén

Philippe Sénac
Représentation 3D de la mosquée de Marcén Fichier Bimx

Homology model of ANR from Pseudomonas aeruginosa

Pseudomonas aeruginosa is a deadly opportunistic human pathogen. The organism codes for different virulence factors and among them is HCN synthesized by HCN synthase enzyme. the enzyme is encoded by the hcnABC operon. It is to be noted that the expression of the genes of the hcnABC operon are regulated by LasR, ANR and RhlR proteins. ANR protein belongs to the FNR family. It works in anaerobic condition. It binds to the promoter DNA as...

SBEM and TEM Membranes (Aug-110)

Matthias Haberl

Calibrated comprehensive model of ROS management improved

Hans Westerhoff, Alexey Kolodkin & Raju Prasad Sharma
RUN the model for steady state. For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500 minutes approx. Plot e.g. ATP. For H2O2 experimental data validation for repeated treatment at 50uM, 150uM, and 300uM. To run the model with different dosing scenarios, one has...

Calibrated comprehensive model of ROS management Improved

Hans Westerhoff, Alexey Kolodkin & Raju Prasad Sharma
This is a model about a ROS network that exhibits five design principles, and has been calibrated so as to predict quantitatively various steady state concentrations. 10191125. Instructions RUN the model for steady state. For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500...

framework model v1_5

Hannah Kinmonth-Schultz
Model associated with the following: Hannah A Kinmonth-Schultz, Melissa J S MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim, An explanatory model of temperature influence on flowering through whole-plant accumulation of FLOWERING LOCUS T in Arabidopsis thaliana, in silico Plants, Volume 1, Issue 1, 2019, diz006, https://doi.org/10.1093/insilicoplants/diz006

Registration Year

  • 2020
    181

Resource Types

  • Model
    181

Affiliations

  • University of California, Riverside
    5
  • Swiss Federal Institute of Aquatic Science and Technology
    4
  • Deutsche Gesellschaft für Internationale Zusammenarbeit
    4
  • University of Leeds
    4
  • National University of Distance Education
    3
  • University of Chicago
    2
  • University of Cologne
    1
  • South African Environmental Observation Network
    1
  • British Geological Survey
    1