PROMALS3D protocols

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

[…] initial alignment using the alignment tool muscle69 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: 5349461
PMID: 28337468
DOI: 10.1016/j.dib.2017.02.047

[…] and used for detection of protein domain conservation and phylogenetic analysis. experimental features human, e.coli and archaea protein helicase sequences were aligned using tcoffee or promals3d..conserved motifs were detected from multiple sequence alignments using weblogo software. phylogenetic analysis were performed using maximum likelihood methods or bayesian methods […]

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

[…] server (la cour et al., 2004). secondary structure prediction and alignment of cacv (km589494), tswv nsm (qld-1255, unpublished), tmv p30 (nc_001367.1), and tvcv p30 (u03387) were carried out using promals3d online (pei and grishin, 2014). nsm sequences were analyzed for predicted coiled-coil domains using an online server (mcdonnell et al., 2006)., to determine intracellular localization […]

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

[…] and limit bias in sample selection. data s1 contains all the sequence information for the tyra orthologs used in figure 2 and figure s1. a structure-guided amino acid alignment was performed in promals3d (pei and grishin, 2007) 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: 5681985
PMID: 29164132
DOI: 10.3389/fmolb.2017.00073

[…] with varying substrate specificities (g. max tyrap; gmpdh1; pdb # 5t8x, h. influenzae tyrap; hipdh; 2pv7, and synechocystis sp. pcc6803 tyraa; synadh; pdb # 2f1k). the amino acid alignment from promals3d was used to construct phylogenetic trees using mega7 (kumar et al., 2016). the full amino acid alignment can be found in data s2. the analyses involved 130 amino acid sequences […]

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

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