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Protocols

ASAView specifications

Information


Unique identifier OMICS_31999
Name ASAView
Alternative name ASA-View
Interface Web user interface
Restrictions to use None
Input format PDB,
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline M. Michael Gromiha
  • person_outline Hamed Fawareh

Publication for ASAView

ASAView citations

 (37)
call_split

Generation of therapeutic protein variants with the human serum albumin binding capacity via site specific fatty acid conjugation

2017
Sci Rep
PMCID: 5740134
PMID: 29269881
DOI: 10.1038/s41598-017-18029-y
call_split See protocol

[…] ously,. Preparation of the plasmid encoding the Uox variant gene containing an amber codon at W160 site (pQE80-Uox-160Amb) was also described previously. The solvent accessibility prediction program (ASA-View) and the protein structure viewer program (PyMOL program) were used to select sites of Uox for AzF incorporation based upon the crystal structure of Uox (PDB ID: 1WS2). ASA-View program predi […]

library_books

Prediction aided in vitro analysis of octa decanoic acid from Cyanobacterium Lyngbya sp. as a proapoptotic factor in eliciting anti inflammatory properties

2017
Bioinformation
PMCID: 5651223
PMID: 29081609
DOI: 10.6026/97320630013301

[…] tures were retrieved from Protein Data Bank (http://www.rcsb.org/pdb) with PDB ID: 1ITV and 1RTG. Solvent accessibility was utilized as a criterion in emancipating the binding nature of the peptides. ASAVIEW [] was used for Solvent accessibility calculations. The online docking program PATCHDOCK [http://bioinfo3d.cs.tau.ac.il/PatchDock/] was used for rigid docking of the proteins with rhodopin an […]

library_books

Molecular docking analysis of UniProtKB nitrate reductase enzyme with known natural flavonoids

2016
Bioinformation
PMCID: 5357572
PMID: 28405127
DOI: 10.6026/97320630012425

[…] ASA plot of nitrate reductase was completed using ASA-View, a database and tools for the solvent accessibility representation in proteins []. A characteristic 2D spiral plot of solvent accessibility provides a convenient graphical view of residues in […]

library_books

Identifying Candidate Targets of Immune Responses in Zika Virus Based on Homology to Epitopes in Other Flavivirus Species

2016
PLoS Curr
PMCID: 5145810
PMID: 28018746
DOI: 10.1371/currents.outbreaks.9aa2e1fb61b0f632f58a098773008c4b

[…] aken as the RFscore. 3D Structural Analysis Structural analyses were performed using the crystal structures of ZIKV E (PDB 5IZ7) and NS1 (PDB 5IY3). Solvent accessibility scores were determined using ASAView: Solvent Accessibility Graphics for proteins (http://www.abren.net/asaview). 3D renderings were generated using Visual Molecular Dynamics (VMD). The online interactive 3D visualization of the […]

library_books

Functional alterations due to amino acid changes and evolutionary comparative analysis of ARPKD and ADPKD genes

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

[…] ondary structure, geometrical appearances and solvent structures of proteins in Protein data bank. The software DSSP estimates entries from PDB (protein data bank) through the entry implementation of ASA view for all the protein or individual chain. The standard used was to add chain or PDB query in the input file, exhibit ASA view plot for co-ordinate or PDB file. The amino acid residues verified […]

library_books

An analysis of horseradish peroxidase enzyme for effluent treatment

2016
Bioinformation
PMCID: 5322315
PMID: 28293074
DOI: 10.6026/97320630012318

[…] arts are also provided by the tool for each amino acid residues with the color coding corresponding to their location i.e. either in the surface or in the core. The ASA plot of HRP was prepared using ASA-View, a database and tools for the solvent accessibility representation in proteins []. […]

Citations

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ASAView institution(s)
Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka, Japan; Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan; Computer Science Department, Zarka Private University, Zarka, Jordan
ASAView funding source(s)
Supported by Advanced Technology Institute Inc., Tokyo.

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