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PINUP specifications


Unique identifier OMICS_30232
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No


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Publication for PINUP

PINUP citations


Incorporation of protein binding effects into likelihood ratio test for exome sequencing data

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

[…] g 10-fold cross-validation on the same data set. The best-performing structure-based classifier achieves an f-measure of 0.46 and an accuracy of 73 %, also outperforming the state-of-the-art approach PINUP (protein interface residue prediction) (f = 0.33, accuracy = 63 % on the same set) [].The variant data provided in the VCF (variant call format) files of the odd numbers of chromosomes for uncor […]


Molecular characterization of HIV 1 Nef and ACOT8 interaction: insights from in silico structural predictions and in vitro functional assays

Sci Rep
PMCID: 4772117
PMID: 26927806
DOI: 10.1038/srep22319

[…] . The CPORT (Consensus Prediction Of interface Residues in Transient complex) bioinformatic tool, a consensus method combining six interface web servers (WHISHY, PIER, ProMate, cons-PPISP, SPIDER and PINUP), was used as interface prediction program. The Nef/ACOT8 docking model was then performed using the HADDOCK (High Ambiguity Driven biomolecular DOCKing) version 2.1 program, based on the previo […]


Structural neighboring property for identifying protein protein binding sites

BMC Syst Biol
PMCID: 4565107
PMID: 26356630
DOI: 10.1186/1752-0509-9-S5-S3

[…] Our method is compared to ProMate and PINUP. The test data is originally used by ProMate [], including 57 unbound proteins and their complexes. The results are reported in Table . The overall Fnat values for our method, PINUP and ProMate […]


Violence: heightened brain attentional network response is selectively muted in Down syndrome

PMCID: 4486123
PMID: 26131023
DOI: 10.1186/s11689-015-9112-y

[…] r signal involved violence.Only two cases of romantic or sexually themed content were present in the 10 cartoons showing differences in attentional activation between the groups: Bugs Bunny holding a pinup image to distract the catcher in a baseball game and Bugs Bunny dressing as a female to lure Elmer Fudd. In both cases, control participants showed significantly higher activation.Comparisons of […]


Progress and challenges in predicting protein interfaces

Brief Bioinform
PMCID: 4719070
PMID: 25971595
DOI: 10.1093/bib/bbv027

[…] ed in a consensus-based classifier. Therefore, some methods have integrated individual interface predictors into one meta framework [, ]. For instance, meta-PPISP [] combines the prediction scores of PINUP, Cons-PPISP and ProMate using linear regression analysis. One review study [] confirmed the superiority of meta-PPISP over its constituent PINUP [], Cons-PPISP [] and ProMate [] with accuracies […]


Algorithmic approaches to protein protein interaction site prediction

PMCID: 4338852
PMID: 25713596
DOI: 10.1186/s13015-015-0033-9

[…] MATE [] and Combined BindML [].More integrative approaches utilize meta-predictors, which combine multiple predictors into a single output score. Meta-PPISP [] combines cons-PPISP [], Promate [], and PINUP [] via a linear regression model taking local environment into account.By adding SPPIDER [] and PPI-PRED [] to that list, metaPPI [] uses the frequency with which its constituent predictors cons […]


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PINUP institution(s)
Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY, USA
PINUP funding source(s)
Supported by National Institutes of Health (R01 GM 066049, 068530), USA, a two-base grant (No. 20340420391) from National Science Foundation of China, by the Center for Computational Research and the Keck Center for Computational Biology at SUNY Buffalo.

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