PROMALS protocols

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PROMALS specifications

Information


Unique identifier OMICS_03745
Name PROMALS
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PROMALS

PROMALS in pipelines

 (9)
2018
PMCID: 5909903
PMID: 29677198
DOI: 10.1371/journal.pone.0195358

[…] cluster were aligned with clustal omega [] and filtered with hhfilter to obtain representative sequences. the representative sequences from of all clusters were collected together and aligned with promals []. the alignment of 161 sequences was subsequently refined with muscle [] and gap-rich columns were removed. a phylogenetic tree was calculated with fasttree [] and visualized with evolview […]

2017
PMCID: 5464003
PMID: 28603670
DOI: 10.7717/peerj.3390

[…] and hhpred () programs. the protein sequences were identified with their uniprotkb identifiers and the nucleotide sequences with their ncbi ones. the sequences were aligned with t-coffee (; ) and promals (; ; ). the secondary structure predictions were performed with psipred (; ; ). multiple sequence alignments were displayed and analyzed with jalview ()., rna and cdna were prepared […]

2014
PMCID: 3969726
PMID: 24368349
DOI: 10.1016/j.bbapap.2013.12.008

[…] prepared as described previously . all experiments were carried out at 25 °c unless otherwise stated. sequence alignments and determination of amino acid identity and similarity were calculated by promals , emboss needle alignment (http://www.ebi.ac.uk/tools/psa/emboss_needle/) and clustal w2 (http://www.ebi.ac.uk/tools/msa/clustalw2/). sequences of type i rm systems were obtained from rebase […]

2014
PMCID: 4159009
PMID: 25062915
DOI: 10.1093/gbe/evu161

[…] aligning sequences from the distantly related four families was complicated. in order to increase the quality of alignment for such highly divergent proteins, structural information has been used by promals-3d software to guide the msa (). as no crystal structures were available for lanl-like proteins, representative sequences of lanl-like proteins venl and ramc were given as input along […]

2012
PMCID: 3281104
PMID: 22359664
DOI: 10.1371/journal.pone.0032138

[…] memsat servers , . the jpred, psipred and sopma servers were used to predict the secondary structure of the selo domains , , . multiple alignments of the selo domain were constructed by using the promals and muscle programs . the former includes predicted secondary structures in the buildup of the alignment, and both employ remote homologues of the aligned sequences. for the multiple […]


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PROMALS in publications

 (56)
PMCID: 5909903
PMID: 29677198
DOI: 10.1371/journal.pone.0195358

[…] cluster were aligned with clustal omega [] and filtered with hhfilter to obtain representative sequences. the representative sequences from of all clusters were collected together and aligned with promals []. the alignment of 161 sequences was subsequently refined with muscle [] and gap-rich columns were removed. a phylogenetic tree was calculated with fasttree [] and visualized with evolview […]

PMCID: 5720693
PMID: 29216252
DOI: 10.1371/journal.pone.0189064

[…] the stability of these structures demonstrate the importance of critical residues in forming a stable frame for the protein structure., to begin, we compared the residue conservation index from the promals[] multiple sequence alignment to the foldability of the same residue produced by ums. following our belief that foldability may be a suitable substitute for residue conservation, […]

PMCID: 5547475
PMID: 28784139
DOI: 10.1186/s12934-017-0737-2

[…] []. ncbi’s conserved domains database (cdd) [] was used for the identification of conserved domains in sequences. t-coffee server [] was used for multiple sequence alignments in combination with promals [] for secondary structure prediction of the sequences., amino acid sequences of three putative afps found in gu3.1.1 and afp5.1 genomes were used as targets for homology modeling using […]

PMCID: 5504000
PMID: 28694498
DOI: 10.1038/s41598-017-05095-5

[…] apo mglu4 tm domain was homology modelled from wt apo mglu5 using rosetta v3.4 with fragments generated with the robetta webserver, following an mglu4-mglu5 tm domain sequence alignment generated by promals-3d, manually curated for improved alignment accuracy (see si)., coordinates for mpep were generated with maestro. autodock v4.2 was used to dock mpep into the apo mglu4 and mglu5 tm domain […]

PMCID: 5442039
PMID: 28545260
DOI: 10.1186/s13568-017-0405-2

[…] udhs and enzymes that had a sequence similarity greater than 60% compared to the udhat were created. from these alignments consensus sequences with coverage of 95 or 80% were created (bioedit and promals) and all amino acids that showed conservation were excluded from mutagenesis. an overview of these five criteria and the amino acids considered for mutagenesis is shown in table . six amino […]


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PROMALS institution(s)
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA

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