PROMALS3D protocols

View PROMALS3D computational protocol

PROMALS3D statistics

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PROMALS3D specifications


Unique identifier OMICS_03731
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PROMALS3D

PROMALS3D in pipelines

PMCID: 5859286
PMID: 29556064
DOI: 10.1038/s41467-018-03503-6

[…] an initial alignment using the alignment tool muscle locally for two iterations. extraneous header information was removed using a custom python script before performing a secondary alignment using promals3d with six additional structure sequences (cyclobutane pyrimidine dimer (cpd) phl from escherichia coli, cpd phl from anacystis nidulans, 6–4 phl from arabidopsis thaliana, cry […]

PMCID: 5387057
PMID: 28443083
DOI: 10.3389/fmicb.2017.00612

[…] () and netnes 1.1 server (). secondary structure prediction and alignment of cacv (km589494), tswv nsm (qld-1255, unpublished), tmv p30 (nc_001367.1), and tvcv p30 (u03387) were carried out using promals3d online (). nsm sequences were analyzed for predicted coiled-coil domains using an online server ()., to determine intracellular localization of viral proteins, we transiently expressed […]

PMCID: 5438488
PMID: 28526057
DOI: 10.1186/s13062-017-0184-3

[…] this sequence set contains both reviewed sequences from swiss-prot and unreviewed sequences from trembl, first multiple sequence alignment was performed using only the five swiss-prot sequences with promals3d (profile multiple alignment with predicted local structures and three-dimensional constraints) [] to obtain an initial alignment. subsequently all the 97 sequences were aligned using […]

PMCID: 5681985
PMID: 29164132
DOI: 10.3389/fmolb.2017.00073

[…] lineages and limit bias in sample selection. data contains all the sequence information for the tyra orthologs used in figure and figure . a structure-guided amino acid alignment was performed in promals3d (pei and grishin, ) using the default parameters with structures of tyra enzymes from plants and microbes with varying substrate specificities (g. max tyrap; gmpdh1; pdb # 5t8x, h. […]

PMCID: 5766207
PMID: 28934483
DOI: 10.1093/nar/gkx609

[…] were removed from subsequent analysis. sequences were clustered at 90% sequence identity using blastclust (). the resulting 323 sequences and the crystal structure of σj were submitted to the promals3d server (). the alignment generated from promals3d was submitted to the consurf server (–) to estimate evolutionary conservation of amino acid residues. consurf estimates evolutionary rates […]

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PROMALS3D in publications

PMCID: 5954444
PMID: 29780242
DOI: 10.1177/1177932218755337

[…] well as random disturbance for the model. the galaxy tbm develops modeling based on 2 stages. on the first stage, the more reliable structures are created selecting models that are aligned with the promals3d and modellercsa models. in the second stage, the loop areas or less reliable areas (called ulr, nonreliable local areas) are detected and remodeled using a refining method based […]

PMCID: 5919972
PMID: 29700357
DOI: 10.1038/s41598-018-25044-0

[…] in cyp5619 family members was carried out as described elsewhere. briefly, the annotated cyp5619 family members were subjected to profile multiple alignment with local structures and 3d constraints (promals3d) to identify the number of invariantly conserved amino acids. the conservation index follows numbers above 4, where 9 is the invariantly conserved amino acid across the input sequences. […]

PMCID: 5908797
PMID: 29674686
DOI: 10.1038/s41467-018-03920-7

[…] in higher eukaryotes (mostly model organisms with fully sequenced genomes) and a few prokaryotes for further analyses., a multiple sequence alignment of selected nhl domains was calculated using promals3d, which takes into account both sequence and structural information. we performed the analysis iteratively, first by calculating the alignment of nhl domain sequences with a support […]

PMCID: 5877779
PMID: 29558430
DOI: 10.3390/ijms19030918

[…] conformation of adic [] (pdb id code: 3l1l). briefly, to construct homology models of lat1, we generated a multiple sequence alignment containing the human slc7 members and the adic structure using promals3d [] (default settings), which was subsequently refined based on structural considerations. initial lat1 models were built using modeller [] and refined using scwrl4 []. the final model […]

PMCID: 5947705
PMID: 29497023
DOI: 10.1107/S2053230X18002819

[…] this observation is supported by the data obtained from anc27. table 8 summarizes the interface areas and table 9 summarizes the numbers of interactions made between different interfaces., using promals3d (pei et al., 2010) to generate a structure-based alignment, conserved regions were analysed. domains are well conserved, but linker regions, especially the linker region between the r […]

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PROMALS3D institution(s)
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA

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