YASARA protocols

View YASARA computational protocol

YASARA statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Molecule viewers chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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

Subtools


  • YARIA Module
  • YASARA Dynamics
  • YASARA Model
  • YASARA NMR Module
  • YASARA Sructure
  • YASARA View
  • YASARA/WHAT IF Twinset

Versioning


Add your version

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

Subtools


  • YARIA Module
  • YASARA Dynamics
  • YASARA Model
  • YASARA NMR Module
  • YASARA Sructure
  • YASARA View
  • YASARA/WHAT IF Twinset

Download


Versioning


Add your version

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 in pipelines

 (3)
2018
PMCID: 5774476
PMID: 29391779
DOI: 10.2147/DDDT.S149973

[…] were executed by using hyperchem 8®, and qsar analysis was performed by using the buildqsar program. preparation of the receptor protein and docking validation method was performed by using yasara (http://www.yasara.org), and preparation of the ligand was performed by using the chemdraw ultra 12.0.2 and marvinsketch programs. the molecular docking process was performed by using […]

2016
PMCID: 5099264
PMID: 27843768
DOI: 10.1016/j.gdata.2016.10.009

[…] protein structure regions. the corresponding position was performed utilizing swiss-port considered separately to receive altered protein model structures. the energy minimizations accomplished by yasara and nomad-ref gromacs using force field energy for the native type protein pkhd1 protein structure and mutant type protein structure based on the protein model rmsd. the complete energy […]

2011
PMCID: 3197589
PMID: 22028795
DOI: 10.1371/journal.pone.0025876

[…] glu→val (e→v). the mutations for 4hhb at the corresponding positions were achieved using swiss-port viewed separately to obtain altered model structures. the energy minimizations were achieved by yasara and nomad-ref gromacs server using force field energy for the native type protein 4hhb and mutant type protein structures from the protein model rmsd. the total energy of native structure 4hhb […]


To access a full list of citations, you will need to upgrade to our premium service.

YASARA in publications

 (404)
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] 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 […]

PMCID: 5942847
PMID: 29702646
DOI: 10.1371/journal.pntd.0006459

[…] generated using the local meta-threading-server (lomets) []. the top 10 models were ranked in order of decreasing confidence score. all models were refined by solvation and energy minimization using yasara []. potential error in the 3d model was evaluated using a ramachandran plot [] and errat [], which were implemented in the structure analysis and verification server […]

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

[…] acid, and is obtained by setting the codon with the highest frequency value to 100%, and all other codons for the same codon are scaled accordingly., homology model of human tspo was built using yasara molecular modelling program version 16.4.6 []. the hm_build.mcr macro of the yasara software was used with the default parameters except the maximum oligomerization state was set to one. […]

PMCID: 5903068
PMID: 29692765
DOI: 10.3389/fmicb.2018.00693

[…] the immunogenic peptides of the predicted protein were assessed by prediction of the tertiary structure of the protein using homology modeling and threading by two different algorithms (i-tasser and yasara) (figure ). in these models, the peptides with higher immunogenic potential from the protein are displayed in different colors (blue, green, red, and yellow). from the structural analysis, […]

PMCID: 5885040
PMID: 29644085
DOI: 10.1038/hgv.2018.16

[…] 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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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