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Protocols

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 citations

 (4)
library_books

Approaches to ab initio molecular replacement of α helical transmembrane proteins

2017
Acta Crystallogr D Struct Biol
PMCID: 5713875
PMID: 29199978
DOI: 10.1107/S2059798317016436

[…] tructure 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, in the […]

library_books

Genomic Selection Improves Response to Selection in Resilience by Exploiting Genotype by Environment Interactions

2016
Front Genet
PMCID: 5062612
PMID: 27790246
DOI: 10.3389/fgene.2016.00178

[…] n the average environment. The breeding values Aint and Asl were bivariate normally distributed as [aintasl]~MVN([00],A⊗[σAint2σAint,AslσAint,AslσAsl2]), where A is the numerator relationship matrix, σAint2, σAsl2 and σAint,Asl are the additive genetic variances and covariance between the two breeding values. Because RN models can be interchanged with multivariate models (De Jong and Bijma, ; Sae- […]

call_split

Comparing co evolution methods and their application to template free protein structure prediction

2016
Bioinformatics
PMCID: 5860252
PMID: 28171606
DOI: 10.1093/bioinformatics/btw618
call_split See protocol

[…] tions 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 dat […]

library_books

Estimation of genetic variance for macro and micro environmental sensitivity using double hierarchical generalized linear models

2013
PMCID: 3734065
PMID: 23827014
DOI: 10.1186/1297-9686-45-23

[…] g per sire, the standard deviations of estimates of σAsl2 and σAv2 decreased substantially, e.g. from 50 to 200 offspring with 54 and 60%, respectively, whereas the standard deviation of estimates of σAint2 decreased only slightly (−10%). When increasing the number of sire families from 50 to 200, standard deviations of estimates of all genetic parameters decreased substantially (from −52 to −58%) […]

Citations

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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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