SAINT2 protocols

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SAINT2 specifications

Information


Unique identifier OMICS_23775
Name SAINT2
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A target sequence, a fragment library and a contact.
Input format FASTA+FLIB+CON
Output data Some structure predictions.
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Saulo H. P. de Oliveira <>

Publication for SAINT2

SAINT2 in pipeline

2016
PMCID: 5860252
PMID: 28171606
DOI: 10.1093/bioinformatics/btw618

[…] the proportion of satisfied predicted contacts can be used to discriminate between correct (tm-score > 0.5) and incorrect models. for this analysis, we used the 10 000 decoys generated using saint2 and metapsicov stage 1 for each of the 41 protein in our pdb-representative dataset. we have considered the proportions of satisfied long-range, short-range and all-range contacts. our results […]


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SAINT2 in publications

 (2)
PMCID: 5713875
PMID: 29199978
DOI: 10.1107/S2059798317016436

[…] of a protein starting purely from its sequence, and not relying on the use of an existing structure as a template. popular examples of ab initio modelling software include rosetta, quark and saint2 (simons et al., 1997; rohl et al., 2004; xu et al., 2012; ellis et al., 2010). ab initio modelling for globular proteins, however, is accurate only for modest chain lengths. for example, […]

PMCID: 5860252
PMID: 28171606
DOI: 10.1093/bioinformatics/btw618

[…] output by psicov, freecontact, ccmpred, bbcontacts, metapsicov stage 1, metapsicov stage 2 and metapsicov hb were used as input for our cotranslational template-free structure prediction method saint2. an outline of our fragment-based de novo structure predictor saint2 is given in ., we generated 10 000 decoys for each set of predicted contacts and for all targets in our pdb-representative […]


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SAINT2 institution(s)
Department of Statiscts, University of Oxford, Oxford, UK; Department of Informatics, UCB Pharma, Slough, UK; Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
SAINT2 funding source(s)
Supported by Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ) - Ciencia Sem Fronteiras - Grant Number: 237656/2012-4; Engineering and Physical Sciences Research Council grant to System Approaches to Biomedical SciencesCentre for Doctoral Training - Grant Number: EP/G037280/1.

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