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IonCom specifications

Information


Unique identifier OMICS_16794
Name IonCom
Interface Web user interface
Restrictions to use None
Input data A structure or sequence file, a selected ligand type, the user’s email address.
Input format PDB, FASTA
Output data The sequence with binding residues highlighted in red color, the predicted binding residues, a 3D view of the structure with binding residues highlighted in red color.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Xiuzhen Hu <>

Information


Unique identifier OMICS_16794
Name IonCom
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A structure or sequence file, a selected ligand type, the user’s email address.
Input format PDB, FASTA
Output data The sequence with binding residues highlighted in red color, the predicted binding residues, a 3D view of the structure with binding residues highlighted in red color.
Computer skills Advanced
Stability Stable
Source code URL https://zhanglab.ccmb.med.umich.edu/IonCom/IonCom.tar.bz2
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Xiuzhen Hu <>

Publication for IonCom

IonCom citations

 (2)
library_books

Candida albicans Sap6 amyloid regions function in cellular aggregation and zinc binding, and contribute to zinc acquisition

2017
PMCID: 5460171
PMID: 28588252
DOI: 10.1038/s41598-017-03082-4

[…] site prediction server (http://bioinfo.cmu.edu.tw/mib/) was used, which predicts metal binding sites using protein three-dimensional structure. sequence based ligand binding prediction software ioncom (http://zhanglab.ccmb.med.umich.edu/ioncom) was used to confirm predicted metal binding sites., four predicted amyloidogenic regions of sap6 (p1–p4) and a scrambled version of the p2 (sp2) […]

library_books

Computational approaches for de novo design and redesign of metal binding sites on proteins

2017
PMCID: 5482196
PMID: 28167677
DOI: 10.1042/BSR20160179

[…] ion-binding sites. a few of them such as metsite [], 3dligandsite [], fragment transformation method [] combine information from both protein sequence and structure. use of ab initio methods as in ioncom [] server has also been recently realized. several helper tools such as metals2 [], metals3 [], findgeo [], checkmymetal (cmm) [] were developed for pairwise structural alignment, database […]


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IonCom institution(s)
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; College of Sciences, Inner Mongolia University of Technology, Hohhot, China; Institute for Data Science and Engineering, East China Normal University, Shanghai, China; School of Mathematical Sciences, Nankai University, Tianjin, China; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
IonCom funding source(s)
This work was supported in part by National Natural Science Foundation of China (30960090, 31260203, 11501306) and National Institute of Health (GM083107 and GM116960).

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