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Protein_ML specifications


Unique identifier OMICS_17508
Name Protein_ML
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Elizabeth Brunk <>

Publication for Protein_ML

Protein_ML in publications

PMCID: 5923437
PMID: 29565808
DOI: 10.3390/v10040143

[…] representative members of the parvovirinae subfamily []. multiple sequence alignment (msa) was carried out using revtrans 2.0 [] with manual adjustment. the alignments of the core of the ns and vp protein ml trees were inferred using iq-tree version 1.4.3 software based on an lg+f+g4 protein substitution model to the core of an ns protein with 145 amino acids and an lg+f+i+g4 protein […]

PMCID: 5805300
PMID: 29420651
DOI: 10.1371/journal.pone.0192422

[…] centrifuged twice with phosphate buffer 5 mm, 0.25 m sucrose (ph 6.5) prepared in 2h2o and kept at 4°c overnight before use to allow a complete h2o-2h2o exchange. twenty microliter pellets (~30 mg protein ml-1) were placed between two caf2 windows separated by 50 μmteflon spacers and transferred to a symta cell mount. the equipment was continuously purged with dry air to minimize […]

PMCID: 5807054
PMID: 29395787
DOI: 10.1016/j.str.2017.12.014

[…] – 22 months old., bovine mitochondria and mitochondrial membranes were prepared as described previously (). complex i was set in the deactive state by incubating the membranes (resuspended to 12 mg protein ml-1 in 20 mm tris-cl ph 7.55, 1 mm edta, 10% glycerol, 0.0075% pmsf) at 37°c for 15 min. then, the membranes were diluted to 5 mg ml-1 in the same buffer but ice cold, and cooled on ice […]

PMCID: 5733092
PMID: 29312166
DOI: 10.3389/fmicb.2017.02447

[…] to olivera-severo et al. (). protein homogeneity was checked by 0.1% sodium dodecyl sulfate 10% polyacrylamide gel electrophoresis (sds-page) (figure ). previous to the experiments, a 0.5 mg−1 solution was dialyzed against 20 mm sodium phosphate 150 mm sodium chloride, ph 7.5 (pbs 7.5), and the buffer from the last dialysis change was used as a negative control […]

PMCID: 5715577
PMID: 28906548
DOI: 10.1111/bph.14033

[…] using calcium green‐5 n (invitrogen, carlsbad, ca, usa) and excitation and emission wavelengths set at 500 and 530 nm respectively. isolated mitochondria (250 μg of mitochondrial protein ml−1) were added to a spectrofluorometer cuvette containing 2 ml of buffer b supplemented with 0.5 μm calcium green‐5 n under constant stirring. upon addition of mitochondria, […]

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Protein_ML institution(s)
Department of Bioengineering, University of California San Diego, CA, USA; School of Biotechnology, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm, Sweden; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark

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