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PredUs specifications

Information


Unique identifier OMICS_08145
Name PredUs
Interface Web user interface
Restrictions to use None
Input data Macromolecular structure data
Input format PDB
Computer skills Basic
Version 1.2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Qiangfeng Cliff Zhang <>

Publications for PredUs

PredUs in publications

 (11)
PMCID: 5889503
DOI: 10.22034/ibj.22.3.180

[…] server provides a tool to predict interfaces from a single protein structure on the basis of local statistical properties of the protein surface derived at the level of atomic groups. the proposed predus software (https://bhapp.c2b2.columbia.edu/predus/) is a flexible, interactive, template-based web server that uses structural information to predict what residues on protein surfaces […]

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

[…] 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 [], prise [], rad-t [] and metappisp [] are summarized in table . performance of those methods, which also includes precision, recall, accuracy and f1 measure, are borrowed from [, , ]. […]

PMCID: 5106212
PMID: 27782885
DOI: 10.7554/eLife.20930.064

[…] from fitting the data to a tetramer model. related to and ., *kds of monomer-to-dimer / dimer-to-tetramer transitions from fitting the data to a tetramer model. related to and ., next, we used the predus2.0 program (), which combines structural homology with residue propensities, to predict ec6 surface residues likely to participate in cis interactions. remarkably, all of the 23 residues […]

PMCID: 4686965
PMID: 26690684
DOI: 10.1371/journal.pcbi.1004580

[…] support vector machines. for instance the vorffip method [] makes use of tens of descriptors and integrates them in a two-step random forest classifier. other machine learning approaches, such as predus [] and efindsiteppi [], rely on the hypothesis that protein-protein interfaces are structurally conserved: they map experimentally characterized interfaces of structurally similar proteins […]

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

[…] are exploited as templates for interface prediction to help overcome the low template coverage that can afflict homology-based methods (d) []., currently there are two main methods in this category, predus [, ] and prise []. predus is an earlier method, which identifies structural neighbours by finding structures with a globally similar fold to the query protein. prise, on the other hand, uses […]


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PredUs institution(s)
Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Howard Hughes Medical Institute, Columbia University, New York, NY, USA

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