2014.igem.org/Team:Goettingen/notebook_drylabCached. and advanced tutorials of the Modeller web page with some modifications. .

www.csb.yale.edu/userguides/datamanip/modeller/manual.pdf1.5 Method for comparative protein structure modeling by Modeller . . . print "

https://www.hindawi.com/journals/bmri/2013/609289/Jun 18, 2013 . Initially ten homology models were generated using Modeller v9.0 [23] and one

https://www.researchgate.net/. /From_10_models_predicted_by_modeller_ which_one_would_be_selectedSimilarFrom 10 models predicted by Modeller which one would be selected ? .

https://salilab.org/archives/modeller_usage/2013/msg00016.htmlCachedSimilarJan 23, 2013 . Re: [modeller_usage] moldpdf, DOPE score and GA341 score . and GA341

onlinelibrary.wiley.com/doi/10.1002/bmb.20396/pdfSimilarchose to use GROMACS [1] for MD simulations, Modeller. [2] for homology . ..

The LRRK2 kinase domain model with the best DOPE score, GA341 score and

https://www.scientistsolutions.com/. /homology-modeling-modellerCachedIt also provides DOPE Score as in Modeller. You can also try on I-Tasser, though

www.nature.com/articles/srep28268/figures/4A gray line indicates the zero value threshold above which, scores are likely to be

https://salilab.org/archives/modeller_usage/2015/msg00055.htmlCachedSimilarApr 20, 2015 . Re: [modeller_usage] DOPE score based model selection . All of them will give

www.pnas.org/content/suppl/2010/05/05/. /pnas.1003587107_SI.pdfMay 5, 2010 . the standard “automodel” routine of MODELLER-9v6 (S4). The models were .

https://salilab.org/modeller/tutorial/basic.htmlCachedSimilarMar 7, 2014 . For example, you could pick the model with the lowest value of the MODELLER

https://springerplus.springeropen.com/articles/10.1186/s40064-016-1891-4Mar 7, 2016 . Comparison of DOPE score, quality factor determination through . by

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242414/We tested DOPE and five other scoring functions by the detection of the native .

vlab.amrita.edu/?sub=3&brch=275&sim=1481&cnt=2CachedSimilarA sequence in PIR format can be read by modeller. . . One can select a model

gpcrm.biomodellab.eu/help/CachedSimilarthe Modeller DOPE score (either of the model itself or of the refined loops). The

https://github.com/salilab/evaluation/blob/. /score_modeller.pyCachedevaluation/python/evaluation/score_modeller.py . This script runs Modeller to

https://modbase.compbio.ucsf.edu/modeval/help.cgi?type=helpCachedSimilarJob Name; Modeller License Key; Email Address; Model File; Alignment File;

https://salilab.org/archives/modeller_usage/2010/msg00030.htmlCachedSimilarJan 27, 2010 . Subject: Re: [modeller_usage] Dope score; From: Modeller . In modeling, the

faculty.concordia.ca/glamoure/pdfs/lab02a_2015.pdfCachedduce a homology model of your own sequence and evaluate it using the DOPE

iitb.vlab.co.in/?sub=41&brch=118&sim=657&cnt=2CachedSimilarAfter the models are created, each of their DOPE Scores and GA341 Score are .

citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.456. CachedMODELLER implements comparative protein structure modeling by . . one with

https://ludwig.guru/s/a+help+of+scoring+modelCachedThese models were validated with the help of Modeller objective function and

. Modeller 9.15 (https://salilab.org/modeller/). For each of the cases, five models

www.bi.up.ac.za/bifcourse2008/Exercises/mod6.pdfCachedAn initial alignment generated using an older version of MODELLER is given in .

academics.wellesley.edu/Chemistry/Don/bambed/lab4.pdfCachedSimilarIn this lab, you will use a program called MODELLER to produce a homology . ..

https://en.wikipedia.org/wiki/Discrete_optimized_protein_energyCachedSimilarDOPE, or Discrete Optimized Protein Energy, is a statistical potential used to

. 300 score defined, 301–302 DOPE score, 302 global and local errors,

www.bonvinlab.org/education/molmod/modelling/CachedMost homology modeling methods, including MODELLER, can use either one or

www.rsc.org/suppdata/mb/c0/c0mb00345j/c0mb00345j.pdfCachedthe ranking of the set of models constructed in MODELLER. 1 . potential

Table 4.1 Alignment score of hydA1 and hydA2 Resolution of 1.39 Å Template .

prime.ucsd.edu/student-voices/reports/2011/DLi_Final_2011.pdfCachedAug 25, 2011 . After the job is done, MODELLER gives three scores: GA341, molpdf, and DOPE.

https://www.csb.pitt.edu/BBSI/2005/poster/lee.pdfCachedThe best model was determined to be the one with the lowest Modeller .

www.bio.iitb.ac.in/~sanjeeva/virtual_lab/Virtual. /procedure.pdfCachedSimilar(worst) to 1.0 (native-like) but the DOPE score values can be more favorable in

bcb.gmu.edu/software/MODELLER/node154.htmlCachedSimilarThe DOPE model score is designed for selecting the best structure from a

https://zhanglab.ccmb.med.umich.edu/bbs/?q=node/4015CachedMay 18, 2016 . . DOPE score, Anolea and QMEAN are poor compared to models from Modeller

sgt.cnag.cat/services/. /pdfs/20071110_Eswar_etal_CPPS2007.pdfCachedSimilarNov 10, 2007 . Keywords: Modeller rprotein structure rcomparative modeling r . .. DOPE score

www.proteinmodelportal.org/?pid=quality_estimationCachedSimilarand reports quality scores such as predicted RMSD and native overlap, along

https://www.omicsonline.org/homology-modelling-of-lycopene-cleavage- oxygenase-the-key-enzyme-of-bixin-production-jcsb.1000059.php. CachedThe 3D structure of the enzyme was predicted by MODELLER program and the

Based on this alignment, 30 models were generated using MODELLER-9.10 and

. Vulgaris) Table 2 Comparative study of DOPE score of five models predicted

www.fiserlab.org/modeller/manual/node253.htmlCachedDOPE uses the standard MODELLER energy function, so any of the arguments .

https://stackoverflow.com/. /perl-script-to-extract-the-lowest-dope-score- from-modeller-output-log-fileCachedAssuming you have all the lines in an array @lines . The following illustrates the

https://www.researchgate.net/. /Can_the_DOPE_score_be_used_to_compare _models_of_different_protein_sequences_using_different_templates2SimilarOr is it only used to pick up the best model among many generated by modeller (

https://i12r-studfilesrv.informatik.tu-muenchen.de/. /Task_5:_Homology_ ModelingCachedSep 2, 2013 . As Modeller quality score, we chose the DOPE score, which is a statistical

https://www.biostars.org/p/235329/CachedYou can assess your models using MODELLER assessment script https://salilab.

kiharalab.org/paper/chenkihara_Prot08.pdfCachedSimilarModeller was run with the default parameter setting. Because a DOPE score

https://academic.oup.com/bioinformatics/article/26/13/1673/200179May 5, 2010 . For each model both the CCF score and the normalized-DOPE score are

https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-3-226Aug 16, 2010 . EasyModeller provides a graphical straight forward interface and . . which all rely

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