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YASARA Structure specifications

Information


Unique identifier OMICS_33600
Name YASARA Structure
Software type Application/Script
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
License Commercial
Computer skills Medium
Stability Stable
Registration required Yes
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Elmar Krieger

YASARA Structure citations

 (57)
library_books

Identification of Key Residues for Enzymatic Carboxylate Reduction

2018
Front Microbiol
PMCID: 5826065
PMID: 29515539
DOI: 10.3389/fmicb.2018.00250

[…] The program YASARA structure (v. 16.6.24, Krieger et al., ) was used to build the models of the A-T-didomain and the full length NcCAR (NcCAR-FL). The target sequence was used to perform a BLAST (Basic Local Alig […]

library_books

Deciphering the Origin, Evolution, and Physiological Function of the Subtelomeric Aryl Alcohol Dehydrogenase Gene Family in the Yeast Saccharomyces cerevisiae

2017
Appl Environ Microbiol
PMCID: 5734042
PMID: 29079624
DOI: 10.1128/AEM.01553-17

[…] In silico modeling of PcAad1p structure was performed using the YASARA Structure software (YASARA Biosciences) with the resolved AKR11C1 structure as the template (). Assessment of modeling quality was carried out using the SWISS-MODEL Web server (http://swissmode […]

call_split

Global computational mutagenesis provides a critical stability framework in protein structures

2017
PLoS One
PMCID: 5720693
PMID: 29216252
DOI: 10.1371/journal.pone.0189064
call_split See protocol

[…] until the cell is neutralized and the requested ion mass fraction 0.9% NaCl (153 mM) is reached. The location of the counter ions does not matter in practice, since they randomly diffuse away later (Yasara Structure manual). The AMBER14 forcefield was used with a periodic cell boundary and the cubic simulation cell of 78.19 x 78.19 x 78.19 Å. Long range electrostatics used a Particle Mesh Ewald a […]

call_split

The Combined Use of in Silico, in Vitro, and in Vivo Analyses to Assess Anti cancerous Potential of a Bioactive Compound from Cyanobacterium Nostoc sp. MGL001

2017
Front Pharmacol
PMCID: 5711831
PMID: 29230175
DOI: 10.3389/fphar.2017.00873
call_split See protocol

[…] c Artificial Reality Application (YASARA), was used for docking calculation between receptors and ligand (Krieger and Vriend, ). The target protein was set in YASARA to run macro file (dock_run.mcr). YASARA structure provides Autodock and VINA tools to dock ligands with proteins (http://www.yasara.org/docking.htm) using a very simple approach (Morris et al., ; Trott and Olson, ). AMBER force field […]

library_books

Multidrug resistance associated protein 4 is a bile transporter of Clonorchis sinensis simulated by in silico docking

2017
PMCID: 5697364
PMID: 29157307
DOI: 10.1186/s13071-017-2523-8

[…] Several MRP4-related PDB structures were found from the PSI-BLAST search with experimentally characterized PDB structures, although there is no solved PDB structure of MRP4 elucidated so far. YASARA Structure selected the templates, such as Bos taurus MRP1 (PDB ID: 5UJA) with 35.2% identity, Caenorhabditis elegans P-gp (PDB ID: 4F4C) with 19.1% identity, MmMRP1 (PDB ID: 4M1M) with 18.9% id […]

call_split

Expression and function of Abcg4 in the mouse blood brain barrier: role in restricting the brain entry of amyloid β peptide

2017
Sci Rep
PMCID: 5645361
PMID: 29042617
DOI: 10.1038/s41598-017-13750-0
call_split See protocol

[…] ce from 82–641 (corresponding to template sequence 66–645). This model was selected and optimized by adding missing hydrogen atoms, tuning side-chains, and energy minimizing using default settings in Yasara Structure (www.YASARA.org). Model quality and optimization were assessed using MolProbity,. The final Abcg4 homodimer was created by aligning an Abcg4 monomer to both ABCG5 and ABCG8 using the […]

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YASARA Structure institution(s)
YASARA Biosciences GmbH, Vienna, Austria

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