MaxSub protocols

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MaxSub specifications

Information


Unique identifier OMICS_11942
Name MaxSub
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Siew Nom <>

Publication for MaxSub

MaxSub in pipelines

 (7)
2013
PMCID: 3742278
PMID: 23867606
DOI: 10.3390/ijms140714892

[…] sequences. control sequences were generated by shuffling the native sequences and subsequences. the quality of structures predicted from each sequence in the dataset was evaluated using tm-score and maxsub. both are automated methods that assign a score between zero and one to a predicted model based on its similarity to the native structure. i-tasser predictions generated from subsequences […]

2007
PMCID: 2048972
PMID: 17877795
DOI: 10.1186/1471-2105-8-345

[…] a single model., the top models selected using the 3d-jury method are shown to be of significantly higher quality (p < 0.01) than those selected using any other method according to the tm-score, maxsub score and gdt score. the top models selected using the modfold method are of significantly higher quality than those of proq-mx, proq-lg and modcheck according to the tm-score (p < 0.01), […]

2007
PMCID: 2048972
PMID: 17877795
DOI: 10.1186/1471-2105-8-345

[…] ρ is measured between predicted and observed model quality scores. the combined observed model quality score was also calculated for each individual model e.g. mean score for each model (tm-score+maxsub+gtd)/3.*the mqap scores for these methods were downloaded from casp7 website; all other mqap methods were run in house during the casp7 experiment. †mqap methods which rely on the comparison […]

2006
PMCID: 1635247
PMID: 16971460
DOI: 10.1093/nar/gkl480

[…] 12.0 of the top confidence hit for ffas03 detections, and at least 20.0 and within 30.0 of the top hit for 3d-jury detections), we found that the best possible parent (as measured by the mammoth maxsub quality of the best 3d-pair () structural alignment derived template) on average increased from 70.6 to 73.4% coverage for psi-blast level targets, from 63.8 to 65.5% for ffas03 level targets, […]

2006
PMCID: 1635247
PMID: 16971460
DOI: 10.1093/nar/gkl480

[…] regime, the k*sync ensemble achieves at least one model of quality close to that of the model produced by the 3d-pair alignment to the best parent (within ∼10% of the full query length by mammoth maxsub). in the ffas03 regime, all 9 of the targets are within this threshold, and in the psi-blast regime it is 58 of the 62 targets. these values contrast with the quality of the best models […]


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MaxSub in publications

 (57)
PMCID: 5877703
PMID: 29534037
DOI: 10.3390/ijms19030842

[…] were validated with the proq, verify3d, and errat tools. the evaluation results for the ca xii model were as follows. proq, lgscore: 5.873 (value >4 implies an extremely good model) and maxsub: 0.585 (values >0.5–<0.8 implies a very good model); verify3d: 3d/1d profile score: 92.49%; errat overall quality factor: 94%. these results confirmed that the predicted ca xii assigned […]

PMCID: 5817056
PMID: 29491860
DOI: 10.3389/fmicb.2018.00233

[…] in the catalytic sites. proq server tools were used to score the constructed models. the lg values of mycth_56237 and mycth_49824 for the constructed models were 4.28 and 3.981, whereas the maxsub values were 0.525 and 0.463, respectively. these results corroborated the 3d structural conformations which could be displayed by pymol. the overall structures of mycth_56237 and mycth_49824 […]

PMCID: 5712783
PMID: 29225431
DOI: 10.6026/97320630013380

[…] for vapc10. prosa web z score for vapc9 and vapc10 was -4.07 and -3.64 respectively, thereby suggesting that the structures are of good quality (). predicted resolution by resprox along with lg and maxsub score determined by proq also indicated the reliability of 3d models. in addition, molprobity revealed that none of the residue possessed bad bonds or β deviations > 0.25a (). the 3d models […]

PMCID: 5624869
PMID: 28970561
DOI: 10.1038/s41598-017-12932-0

[…] allowed regions (beige), and only 0.3% residues of modelled protein are within the disallowed regions (white). protein quality predictor (proq server) indicated lgscore of “extremely good model” and maxsub of “very good model” quality measures. z-score for the predicted model is within the range of scores typically found for the native proteins of similar size (supplementary fig. ) […]

PMCID: 5393879
PMID: 28414753
DOI: 10.1371/journal.pone.0175835

[…] levels over time on pd was associated with subsequent development of pmf. we defined two variables: 1) d1u ccl18 (the last ccl18 value in effluent minus the baseline level in each patient); and 2) maxsub ccl18 (maximum ccl18 level in effluent during the follow-up minus the minimum ccl18 level measured in each patient). a cox hazard analysis of these variables revealed that an increase in ccl18 […]


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MaxSub institution(s)
Department of Chemistry, Ben Gurion University, Beer-Sheva, Israel

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