PSIVER protocols

View PSIVER computational protocol

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PSIVER specifications

Information


Unique identifier OMICS_08135
Name PSIVER
Interface Web user interface
Restrictions to use None
Input data Protein sequences
Input format FASTA
Computer skills Basic
Stability No
Maintained No

Publication for PSIVER

PSIVER in pipeline

2014
PMCID: 4096751
PMID: 24997568
DOI: 10.1186/1756-0500-7-435

[…] (http://toolkit.tuebingen.mpg.de/hhpred/, with the hmm database of pdb70_18dec10) [] using the three segments defined in figure  as queries., interaction sites on big3 and phb2 were predicted using psiver []. the default threshold of 0.390 was used in this study. interacting pair positions between the two proteins were predicted using ppipp [] with default parameters., the helical wheel […]


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PSIVER in publications

 (10)
PMCID: 5512694
PMID: 28555617
DOI: 10.1038/ncomms15427

[…] among different species. the conservation was assessed by comparing the human, mouse, chimpanzee, monkey, cow, dog and rat sequences with pam500, as described in hou et al. in addition, we also used psiver, a method to predict residues that bind to other proteins, to confirm that the predicted riibds included potential protein-binding sites. the default threshold of 0.390 was used in the present […]

PMCID: 5133940
PMID: 27879651
DOI: 10.3390/ijms17111946

[…] gained more attention due to the rapid growth of structural information (in pdb). in this review, the following individual studies are taken as examples., case 1: a prediction server of ppis named psiver [] predicts binding residue protein pairs by using the naive bayes (nb) classifier and kernel density estimation (kde) with two distinct features: position-specific scoring matrix (pssm) […]

PMCID: 5133515
PMID: 27980649
DOI: 10.1186/s12919-016-0043-8

[…] respectively. our best-performing sequence-based classifier for hetero-oligomeric interactions reports an f-measure of 0.38 and an accuracy of 64 %, outperforming the state-of-the-art approach psiver (a server for the prediction of protein–protein interaction sites in protein sequences) (f = 0.36, accuracy = 60 % on the same set) []., similarly, for the structure-based method, 4 random […]

PMCID: 5063617
PMID: 27582384
DOI: 10.1091/mbc.E16-05-0332

[…] [ ] and modeller [ ]) and calculated their surface properties (ef-surf [ ]). the structural model of lim was placed on the jrab-c model such that the protein-binding residues in lim predicted by psiver () were in contact with the putative lim-binding regions in the jrab-c model. the rab13 model was placed on jrab-c based on the known structures of the three rab–effector complexes., […]

PMCID: 4677168
PMID: 26697220
DOI: 10.1155/2015/978193

[…] meanwhile, there are other existing outstanding computational methods to predict interface residues, we compared our method with these reported prediction methods, including isis [], sppider [], and psiver [], which were tested on the same independent test set dtestset72; showed the best results of each model. then, we also compared our model with several other machine learning algorithm […]


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PSIVER institution(s)
National Institute of Biomedical Innovation, Osaka, Japan

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