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SPPIDER specifications

Information


Unique identifier OMICS_08137
Name SPPIDER
Alternative name Solvent accessibility based Protein-Protein Interface iDEntification and Recognition
Interface Web user interface
Restrictions to use None
Input data ID, file
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Solvent accessibility based Protein-Protein Interface iDEntification and Recognition

SPPIDER citations

 (23)
library_books

CoeViz: A Web Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices

2018
PMCID: 5798608
PMID: 29423399
DOI: 10.3390/data3010004

[…] The following tools were used to retrieve additional information about specific residues based on the resolved structures: POLYVIEW-2D [] for the identification of metal and DNA binding residues and SPPIDER [] for the analysis of protein–protein interaction sites. […]

library_books

Utilizing knowledge base of amino acids structural neighborhoods to predict protein protein interaction sites

2017
BMC Bioinformatics
PMCID: 5731498
PMID: 29244012
DOI: 10.1186/s12859-017-1921-4

[…] dataset as well. For the PlaneDimers and TransComp1 datasets, surface residues were defined as those with RASA≥0.05 while for DS188 the rule was RASA>0.Results showing the comparison of INSPiRE with SPPIDER [], PresCont [] and MetaPPISP [] in terms of MCC on the PlaneDimers and TransComp1 datasets are in Table . The MCC values of the other methods are taken from []. The comparison with PredUs [], […]

library_books

Ebola virus VP24 interacts with NP to facilitate nucleocapsid assembly and genome packaging

2017
Sci Rep
PMCID: 5550494
PMID: 28794491
DOI: 10.1038/s41598-017-08167-8

[…] s: Voronoi Random Forest Feedback Interface Predictor (VORFFIP), Consensus Protein-Protein Interaction Site Predictor (cons-PPISP), , Meta Protein-Protein Interaction Site Predictor (meta-PPISP), and Solvent Accessibility based Protein-Protein Interface Identification and Recognition (SPPIDER). The consensus predictions of each method were combined to generate the prediction shown in Supplementary […]

library_books

Prediction of a highly deleterious mutation E17K in AKT 1 gene: An in silico approach

2017
PMCID: 5637233
PMID: 29114575
DOI: 10.1016/j.bbrep.2017.04.013

[…] mutant AKT1 models having highly deleterious nsSNPs (A255T, E17K and E319G). A further deeper insight of the solvent accessibility and secondary structures of these mutant AKT1models were gained from SPPIDER. This tool identified one mutant AKT1 model having E17K nsSNP with deviated accessible surface area from buried to exposed, thus increasing the solvent accessibility of the mutant model. Amino […]

library_books

Integrative modelling of TIR domain containing adaptor molecule inducing interferon β (TRIF) provides insights into its autoinhibited state

2017
Biol Direct
PMCID: 5397763
PMID: 28427457
DOI: 10.1186/s13062-017-0179-0

[…] veals presence of two clefts. Residues lining the major cleft are mostly acidic, but the residues within the cleft are mainly non-polar residues. Binding site prediction algorithms, meta-PPISP [] and SPPIDER [], pinpoint certain sets of residues which cluster into two distinct regions on the N-terminal domain. These regions are located opposite to each other. One region (denoted as Region I) inclu […]

library_books

Steric Clash in the SET Domain of Histone Methyltransferase NSD1 as a Cause of Sotos Syndrome and Its Genetic Heterogeneity in a Brazilian Cohort

2016
Genes
PMCID: 5126782
PMID: 27834868
DOI: 10.3390/genes7110096

[…] ion regarding the effect of point mutations on the NSD1 protein function could already be obtained at the sequence level using in silico approaches. We used in silico tools including I-Mutant 2.0 [], SPPIDER [], Polyphen [], PANTHER [] and SIFT [] (on all the mutations in ) to calculate the relative residue stability constants for the wild-type (WT) protein and its mutant forms. These methods are […]

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SPPIDER institution(s)
Division of Biomedical Informatics, Children's Hospital Research Foundation, Cincinnati, OH, USA

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