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Protocols

SPIDER specifications

Information


Unique identifier OMICS_13243
Name SPIDER
Alternative names Sequence-based Prediction of Local and Nonlocal Structural Features for Proteins, SPIDER2, SPIDER3
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Protein sequence
Input format Fasta
Output data Secondary structure predictions, accessible surface area predictions, angle predictions
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Yaoqi Zhou
  • person_outline Yuedong Yang

Additional information


Version 2 is available on http://sparks-lab.org/server/SPIDER2/

Information


Unique identifier OMICS_13243
Name SPIDER
Alternative names Sequence-based Prediction of Local and Nonlocal Structural Features for Proteins, SPIDER2, SPIDER3
Software type Package/Module
Interface Application programming interface
Restrictions to use Academic or non-commercial use
Input data A protein sequence.
Input format Fasta
Output data Secondary structure predictions, accessible surface area predictions, angle predictions
Operating system Unix/Linux, Mac OS
Programming languages MATLAB, Python
Computer skills Advanced
Stability Stable
Requirements
Numpy
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Yaoqi Zhou
  • person_outline Yuedong Yang

Additional information


Version 2 is available on http://sparks-lab.org/server/SPIDER2/

Publications for Sequence-based Prediction of Local and Nonlocal Structural Features for Proteins

SPIDER citations

 (14)
library_books

REDIdb 3.0: A Comprehensive Collection of RNA Editing Events in Plant Organellar Genomes

2018
Front Plant Sci
PMCID: 5904370
PMID: 29696033
DOI: 10.3389/fpls.2018.00482

[…] eb standards (https://d3js.org/). Functional domains have been detected using InterPro engine (Jones et al., ), while protein secondary structures have been predicted using the stand-alone version of Spider2 program (Yang et al., ).All the scripts to parse multiple alignments, InterPro html files and Spider2 outputs have been created in Python. Scripts used to extract RNA editing positions from Ge […]

call_split

The importance of negative determinants as modulators of CK2 targeting. The lesson of Akt2 S131

2018
PLoS One
PMCID: 5832243
PMID: 29494643
DOI: 10.1371/journal.pone.0193479
call_split See protocol

[…] the heavy atoms fixed at their crystallographic positions.To predict the structure of Akt1/2 peptides, a combination of different Neural Network based algorithms has been used (Jpred [], PsiPred [], Spider []). The final result was obtained through a consensus strategy where the prediction was confirmed at 90% by all the techniques considered, unless differently indicated. The peptides 3D structu […]

library_books

iDTI ESBoost: Identification of Drug Target Interaction Using Evolutionary and Structural Features with Boosting

2017
Sci Rep
PMCID: 5735173
PMID: 29255285
DOI: 10.1038/s41598-017-18025-2

[…] This feature is the normalized count or frequency of the structural motifs present at the amino-acid residue positions. There are three types of motifs: α-helix (H), β-sheet (E) and random coil (C). SPIDER2 returns a vector SS of dimension L × 1 containing this information. Thus we can define this feature as following:3SS‐Composition(i)=1L∑j=1Lcij,1≤i≤3Here, L is the length of the protein andcij= […]

library_books

Structure of the transcription activator target Tra1 within the chromatin modifying complex SAGA

2017
Nat Commun
PMCID: 5691046
PMID: 29146944
DOI: 10.1038/s41467-017-01564-7

[…] rvation scores between 11 (maximum value) and 9. A consensus secondary structure prediction of the HEAT domain of PpTra1 was built using four individual predictions obtained using the programs JPred, SPIDER,, and HHpred, using either the sequence of PpTra1 or the previously built MSA as input. The predicted lengths of helices were compared to the lengths of helices fitted in the density map. The c […]

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

[…] ediction method for identification of DNA-binding proteins. We have used evolutionary and structural features for the classification extracted from PSSM files and SPD files generated by PSI-BLAST and SPIDER2, respectively. We also used recursive feature elimination to select an optimal set of features. The final model for prediction was developed using Support Vector Machine (SVM) with linear kern […]

library_books

Revision of Failed Rotator Cuff Reconstruction With a Large Humeral Head Cyst

2017
PMCID: 5799591
PMID: 29430398
DOI: 10.1016/j.eats.2017.07.024

[…] Under general anesthesia, the patient is positioned in the lateral decubitus position. The arm position is maintained in 45° of abduction using the SPIDER2 Arm positioner (TENET Medical Products, Smith & Nephew, Andover, MA) (). After marking the skin for the portals, a posterior viewing portal is created. The camera is introduced through the pos […]

Citations

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SPIDER institution(s)
Signal Processing Laboratory, School of Engineering, Griffith University, Brisbane, QLD, Australia; Department of Psychiatry, Medical Research Center, University of Iowa, Iowa City, IA, USA; Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, QLD, Australia; School of Engineering and Physics, University of the South Pacific, Private Mail Bag, Laucala Campus, Suva, Fiji; Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou University, Dezhou, China; National ICT Australia (NICTA), Brisbane, QLD, Australia; Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast Campus, Southport, QLD, Australia
SPIDER funding source(s)
Supported by National Health and Medical Research Council (1059775) of Australia and Australian Research Council’s Linkage Infrastructure, Equipment and Facilities funding scheme (project number LE150100161), the Taishan Scholars Program of Shandong province of China, National Natural Science Foundation of China (61540025) and National Natural Science Foundation of China (61271378).

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