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Protocols

AllosMod specifications

Information


Unique identifier OMICS_34429
Name AllosMod
Interface Web user interface
Restrictions to use None
Input data A protein or DNA/RNA sequence.
Input format PDB
Output data A MODELLER script, a unique starting structure, a restraint file containing interactions that will define the energy landscape, log files, and other output files.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Andrej Sali
  • person_outline Patrick Weinkam

Publication for AllosMod

AllosMod citations

 (5)
library_books

C1q and Mannose Binding Lectin Interact with CR1 in the Same Region on CCP24 25 Modules

2018
Front Immunol
PMCID: 5845983
PMID: 29563915
DOI: 10.3389/fimmu.2018.00453

[…] tio envelopes were calculated using DAMMIF and also GASBOR, to make use of good data quality in the high angle region. An intitial model of CCP24-25 was obtained by homology modeling using the server ALLOSMOD () and the crystal structure of the CRRY complement receptor (2xrb) as starting template. Two N-glycans were modeled at positions Asn 1534 and Asn 1540 according to the prediction of the NetN […]

call_split

Intermittent C1 Inhibitor Deficiency Associated with Recessive Inheritance: Functional and Structural Insight

2018
Sci Rep
PMCID: 5772639
PMID: 29343682
DOI: 10.1038/s41598-017-16667-w
call_split See protocol

[…] glycans (a total of three are bound to the serpinic domain of C1-INH, http://www.uniprot.org/uniprot/P05155) to check for steric clashes. The virtual glycosylation was performed with the help of the Allosmod online server (https://modbase.compbio.ucsf.edu/allosmod/).Molecular graphics were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualizatio […]

library_books

Structural Mechanism for Modulation of Synaptic Neuroligin Neurexin Signaling by MDGA Proteins

2017
Neuron
PMCID: 5563082
PMID: 28817804
DOI: 10.1016/j.neuron.2017.07.040

[…] ded to the resulting assembled model using the MODELER () “Model/Refine Loops” routine as implemented in Chimera ().Coarse-grained molecular dynamics (MD) simulations were performed using the program Allosmod (). Five independent runs were performed, each consisting of 30 independent trajectories generating 100 models. From this total pool of 15,000 models, automated selection of the minimal set o […]

call_split

Repulsive Guidance Molecule is a structural bridge between Neogenin and Bone Morphogenetic Protein

2015
PMCID: 4456160
PMID: 25938661
DOI: 10.1038/nsmb.3016
call_split See protocol

[…] FN56M binary subcomplex were then extracted from the completed BMP2-eRGMB–NEO1FN56M model. All-atom ensemble modeling of NEO1FN56M, eRGMB, eRGMB–NEO1FN56M and BMP2–eRGMB–NEO1FN56M was performed using AllosMod; and in each case, 50 independent ensembles of 100 models were generated. From this pool, automated selection of the minimal set of models satisfying the scattering data was performed using M […]

library_books

Structural basis for extracellular cis and trans RPTPσ signal competition in synaptogenesis

2014
Nat Commun
PMCID: 4239663
PMID: 25385546
DOI: 10.1038/ncomms6209

[…] further modelling. Missing loops and N- and C termini were added in extended conformations using the program Modeller. All-atom simulations of RPTPσ Ig1-FN3 and sEcto was performed using the program AllosMod. For each starting structure, 30 independent pools of 100 models were generated. For the combined pool, calculation and fitting of scattering patterns was performed using the program FoXS, an […]

Citations

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AllosMod institution(s)
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA; Rinat Laboratories, Biotherapeutics and Bioinnovation Center, Pfizer, Inc., South San Francisco, CA, USA
AllosMod funding source(s)
Supported by Pfizer, Inc.

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