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BindUP specifications

Information


Unique identifier OMICS_11964
Name BindUP
Interface Web user interface
Restrictions to use None
Input data BindUP server has two modes of usage, a single protein mode and a batch mode. In the single protein mode, BindUP predicts the NA-binding propensity for a given protein structure. The user can choose whether to calculate all the protein chains of the structure (each chain is calculated separately) or to select a specific chain identifier. The structure can be provided as either a PDB ID or as a user-defined coordinate file (of a known structure or a structural model) in PDB format. In the batch mode, BindUP gets a list of protein structures and calculates the requested electrostatic patches and the NA-binding prediction for each structure. The structures should be provided as PDB IDs only, pasted into the browser or uploaded as a text file.
Output data BindUP calculation is performed on each protein chain separately. The results, for each requested protein chain, include the NA-binding prediction and the requested electrostatic patches on the protein surface.
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Inbal Paz

Publication for BindUP

BindUP citations

 (3)
library_books

Characterization of the African Swine Fever Virus Decapping Enzyme during Infection

2017
J Virol
PMCID: 5709586
PMID: 29021398
DOI: 10.1128/JVI.00990-17

[…] binding, possibly due to the lack of decapping activity, and consequently the lack of RNA degradation, expected in this variant.To predict the most likely RNA-binding surface within ASFV-DP, we used BindUP software (Israel Institute of Technology), which calculates the local electrostatic potential to predict protein surfaces with potential to bind RNA ( and ). BindUP identified two large positiv […]

library_books

HMMBinder: DNA Binding Protein Prediction Using HMM Profile Based Features

2017
Biomed Res Int
PMCID: 5706079
PMID: 29270430
DOI: 10.1155/2017/4590609

[…] several of them: DNABinder [], DNA-Prot [], iDNA-Prot [], iDNA-Prot|dis [], DBPPred [], iDNAPro-PseAAC [], PseDNA-Pro [], Kmer1 + ACC [], Local-DPP [], SVM-PSSM-DT [], PNImodeler [], CNNsite [], and BindUP []. Most of these methods have used sequence, profile, or structure based features. In structural feature based methods in the literature, features used were structural motifs, electrostatic po […]

library_books

iDNAProt ES: Identification of DNA binding Proteins Using Evolutionary and Structural Features

2017
Sci Rep
PMCID: 5668250
PMID: 29097781
DOI: 10.1038/s41598-017-14945-1

[…] their model. Wei et al. proposed Local-DPP by using Random Forest classifier on local pseudo position specific scoring matrix features. Among other recent works are SVM-PSSM-DT, PNImodeler, CNNsite, BindUP, etc.One of the most important but also most difficult problems in computational biology is how to express a biological sequence with a discrete model or a vector, yet still keep considerable s […]

Citations

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BindUP institution(s)
Department of Biology, Technion—Israel Institute of Technology, Technion City, Haifa, Israel
BindUP funding source(s)
Israel Science Foundation (ISF) [1623/12]

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