MetaDBSite specifications

Information


Unique identifier OMICS_08397
Name MetaDBSite
Interface Web user interface
Restrictions to use None
Input data Protein sequence
Input format FASTA, Raw
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Bingding Huang <>

Publication for MetaDBSite

MetaDBSite in publications

 (4)
PMCID: 5664376
PMID: 29181384
DOI: 10.1155/2017/2763259

[…] phi/psi ramachandran plot and 3d id score was calculated at procheck server (http://services.mbi.ucla.edu/saves/). active binding amino acid residues within sant domains were predicted by the online metadbsite database []. pymol-educational software (http://www.pymol.org/) was used to visualize the predicted parameters in 3d structure. motif scan (http://myhits.isb-sib.ch/cgi-bin/motif_scan) web […]

PMCID: 4683125
PMID: 26681179
DOI: 10.1371/journal.pcbi.1004639

[…] prediction approaches have been summarized in . slow programs dr_bind1 and rbrdetector were only tested on part of the datasets and the results are provided in the supplementary information. metadbsite[] shows same result as bindn and was not tested explicitly., pssm: position specific scoring matrix derived from sequence alignment, rp: residue propensity, asa: accessible surface area, […]

PMCID: 4394471
PMID: 25756377
DOI: 10.3390/ijms16035194

[…] the frequently used clustering program contains blastclust (available from the national center for biotechnology information, ncbi), the pisces web server [], and the h-cd-hit program []. using the metadbsite method, the protein–dna complexes with a resolution better than 3.0 å were submitted to h-cd-hit to obtain a nonredundant data set, which was first clustered at a high identity (90%), […]

PMCID: 3763535
PMID: 23788679
DOI: 10.1093/nar/gkt544

[…] or available standalone programs (). the methods are bindn (), bindn+ (), bindn-rf (), dbs-pred (), dbs-pssm (), dnabindr (), dp-bind with three categories, binary, blosum and pssm encoding (), metadbsite () and naps (). the details about the name, features, technique, reference and link for the methods used in the present work are listed in supplementary table s1. these methods used […]


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MetaDBSite institution(s)
Systems Biology Division, Zhejiang-California International NanoSystems Institute, Zhejiang University, Hangzhou, China
MetaDBSite funding source(s)
Ministry of Science and Technology of China (grant No. 2008DFA11320) and EU 7th framework Marie Curie Action IRESE program (grant NO. 247097)

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