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Protocols

ProQ3D specifications

Information


Unique identifier OMICS_14652
Name ProQ3D
Alternative name ProQ3
Interface Web user interface
Restrictions to use None
Input data Structure models in PDB format, the amino acid target sequence in FASTA format
Input format PDB, FASTA
Output data The global and local scores of the models to be predicted
Output format TXT, ZIP
Programming languages Python, R
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Arne Elofsson
  • person_outline Nanjiang Shu
  • person_outline David Menendez Hurtado

Information


Unique identifier OMICS_14652
Name ProQ3D
Alternative name ProQ3
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Structure models in PDB format, the amino acid target sequence in FASTA format.
Input format PDB, FASTA
Output data The global and local scores of the models to be predicted.
Output format TXT, ZIP
Operating system Unix/Linux
Programming languages Python, R
Computer skills Advanced
Stability Stable
Requirements
Rosetta, zoo, EMBOSS, numpy, h5py, keras
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Arne Elofsson
  • person_outline Nanjiang Shu
  • person_outline David Menendez Hurtado

Publications for ProQ3D

ProQ3D citations

 (7)
library_books

Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures

2017
Int J Mol Sci
PMCID: 5751226
PMID: 29206185
DOI: 10.3390/ijms18122623

[…] re manageable number and processed manually to determine the highest quality predicted pose.Although many different forms of tertiary model evaluation exist; such as those implemented in ModFOLD6 [], ProQ3 [,] and others [], recent progression onto quaternary protein modelling means that a reliable generic quaternary structure model quality assessment method has yet to be developed. The ZDOCK meth […]

library_books

An overview of comparative modelling and resources dedicated to large scale modelling of genome sequences

2017
Acta Crystallogr D Struct Biol
PMCID: 5571743
PMID: 28777078
DOI: 10.1107/S2059798317008920

[…] Q2 combines evolutionary information, multiple sequence alignment data and structural features from the model using a support vector machine (SVM) to assess the quality (Ray et al., 2012). The recent ProQ3 uses a deep-learning method to combine ProQ2 with Rosetta energy terms (Leaver-Fay et al., 2011) and has been shown to be superior to ProQ2 (Uziela et al., 2016, 2017). DeepQA is another deep-le […]

call_split

Large scale structure prediction by improved contact predictions and model quality assessment

2017
Bioinformatics
PMCID: 5870574
PMID: 28881974
DOI: 10.1093/bioinformatics/btx239
call_split See protocol

[…] der to make this score comparable between targets, we normalize it by the length of the input protein sequence and refer to it as CNS-contact.In addition to using the CNS contact energy, we also used ProQ3D () and Pcons (). Further, we developed PcombC a linear combination between the scores of ProQ3D, Pcons and PPV, similar to what we used in CASP4 () and CASP5 (). Coefficients have been determin […]

call_split

ProQ3: Improved model quality assessments using Rosetta energy terms

2016
Sci Rep
PMCID: 5048106
PMID: 27698390
DOI: 10.1038/srep33509
call_split See protocol

[…] ew predictors: one that uses full-atom model (“ProQRosFA”) and one that uses centroid model (“ProQRosCen”). In addition, we developed a third predictor that combines ProQRosFA, ProQRosCen and ProQ2 (“ProQ3”).The new predictors use the same method to train a linear SVM as was used in ProQ2. Here the quality of each residue is described using the S-score and used as a target function. However, the d […]

call_split

Guided self help cognitive behavioral intervention for VoicEs (GiVE): study protocol for a pilot randomized controlled trial

2016
PMCID: 4960672
PMID: 27456976
DOI: 10.1186/s13063-016-1494-y
call_split See protocol

[…] iefs about themselves. The BCSS self-scale has 12 items and has strong internal consistency when given to clinical participants (α = 0.84).The Person’s Relating to Others Questionnaire short version (PROQ3) [] measures social relating (person to person) in terms of their proximity and power. The questionnaire includes 48 items, and all scales show acceptable levels of internal consistency (all sca […]

library_books

Relating therapy for voices (the R2V study): study protocol for a pilot randomized controlled trial

2014
PMCID: 4150948
PMID: 25128004
DOI: 10.1186/1745-6215-15-325

[…] easured by the Choice of outcome in CBT for psychoses [CHOICE] questionnaire), relating to people in the social world (measured by the shorter version of the Persons Relating to Others Questionnaire [PROQ3]), and mood and anxiety (measured by the Hospital Anxiety and Depression Scale [HADS]); and 4) Improvements in relating to people in the social world will be associated with improvements in rela […]

Citations

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ProQ3D institution(s)
Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden; Bioinformatics Short-term Support and Infrastructure (BILS), Science for Life Laboratory, Solna, Sweden; Department of Physics, Chemistry and Biology (IFM) /Bioinformatics, Linkoping University, Linkoping, Sweden
ProQ3D funding source(s)
Supported by grants from the Swedish Research Council (VR-NT 2016-03798 and 2012-5270) and Swedish e-Science Research Center.

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