YASARA statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

YASARA specifications

Information


Unique identifier OMICS_05077
Name YASARA
Alternative name Yet Another Scientific Artificial Reality Application
Software type Package/Module
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
License Commercial
Computer skills Medium
Stability Stable
Maintained Yes

Subtool


  • YASARA/WHAT IF Twinset

Versioning


No version available

Documentation


Maintainers


  • person_outline Elmar Krieger
  • person_outline YASARA Team

Additional information


Several subtool, including a free tool, are available. Free subtool: http://www.yasara.org/viewdl.htm

Information


Unique identifier OMICS_05077
Name YASARA
Alternative name Yet Another Scientific Artificial Reality Application
Interface Graphical user interface
Restrictions to use License purchase required
Computer skills Medium
Stability Stable
Mobile operating system Android
Maintained Yes

Subtool


  • YASARA/WHAT IF Twinset

Download


download.png

Versioning


No version available

Documentation


Maintainers


  • person_outline Elmar Krieger
  • person_outline YASARA Team

Additional information


Several subtool, including a free tool, are available. Free subtool: http://www.yasara.org/viewdl.htm

Publication for Yet Another Scientific Artificial Reality Application

YASARA citations

 (432)
library_books

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine based chemotherapy

2018
BMC Cancer
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] al/mol) of the protein by the SNP as predicted by FoldX from 5 runs [] is significant i.e. more than 0.5 kcal/mol or less than − 0.5 kcal/mol. The menu option “Mutate residue” in the FoldX plugin for YASARA [] was used to predict free energy changes of the protein when the wild-type amino acid is mutated to another amino acid to predict the effect of SNPs on protein structure. The structure of the […]

library_books

Characterization of a novel organic solute transporter homologue from Clonorchis sinensis

2018
PLoS Negl Trop Dis
PMCID: 5942847
PMID: 29702646
DOI: 10.1371/journal.pntd.0006459

[…] The top 10 3D models of CsOST-N and -C domains were built based on multiple templates using LOMETS [] and refined using YASARA energy minimization []. A final 3D model of each CsOST domain was determined according to stereochemical quality assessment as well as high structural similarity indicated as the TM-score on st […]

library_books

Effects of genetic variants in the TSPO gene on protein structure and stability

2018
PLoS One
PMCID: 5895031
PMID: 29641545
DOI: 10.1371/journal.pone.0195627

[…] ations on TSPO protein structure and stability. The energy minimised structures of the native and mutant TSPO proteins were used as starting points for the MD simulations, which were carried out with YASARA software using the md_runmembrane.mcr macro and the AMBER04 force field.The TSPO simulation was set up automatically by first scanning the protein for exposed transmembrane helices. Based on th […]

library_books

A Carbohydrate Moiety of Secreted Stage Specific Glycoprotein 4 Participates in Host Cell Invasion by Trypanosoma cruzi Extracellular Amastigotes

2018
Front Microbiol
PMCID: 5903068
PMID: 29692765
DOI: 10.3389/fmicb.2018.00693

[…] The three-dimensional structure of the putative Ssp-4 sequenced by mass spectrometry was modeled using I-Tasser () and Yasara. The model with the highest C-score from I-Tasser and the hybrid model from Yasara were selected for structural analysis. The solvent-accessible surface area (SASA) of each amino acid was calcu […]

call_split

Protein molecular modeling shows residue T599 is critical to wild type function of POLG and description of a novel variant associated with the SANDO phenotype

2018
Hum Genome Var
PMCID: 5885040
PMID: 29644085
DOI: 10.1038/hgv.2018.16
call_split See protocol

[…] g. Monte Carlo simulations were performed on the mutant to allow local regional changes after the p.T599P and p.T599E variants were introduced.The X-ray refinement for Monte Carlo was built using the YASARA SSP/PSSM method. The structure was relaxed to the YASARA/Amber force field using knowledge-based potentials within YASARA. The side chains and rotamers were adjusted with knowledge-based potent […]

call_split

GATA4 Variants in Individuals With a 46,XY Disorder of Sex Development (DSD) May or May Not Be Associated With Cardiac Defects Depending on Second Hits in Other DSD Genes

2018
PMCID: 5893726
PMID: 29670578
DOI: 10.3389/fendo.2018.00142
call_split See protocol

[…] Since the structure of GATA4 protein is not known, a hybrid homology model of the protein was made using YASARA () and AMBER. Three rounds of PSI-BLAST were performed with the GATA4 amino acid sequence (NP_002043) to build a position-specific scoring matrix, and then a search of protein structure databas […]

Citations

Looking to check out a full list of citations?

YASARA institution(s)
Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
YASARA funding source(s)
Supported by the European Commission within its FP7 Programme, under the thematic area KBBE-2011-5 with contract number 289350.

YASARA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review YASARA