STRAP protocols

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STRAP specifications

Information


Unique identifier OMICS_03657
Name STRAP
Alternative name STRuctural Alignments of Proteins
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Christoph Gille <>

Publications for STRuctural Alignments of Proteins

STRAP in pipelines

 (5)
2016
PMCID: 4909266
PMID: 27304881
DOI: 10.1371/journal.pone.0156838

[…] serovar typhimurium) [1adr_a, 2r1j_l, 3jxb_c] []. hhpred [] and raptorx [–] were used to predict tertiary structure and binding sites. these predicted structures were then superimposed using strap [] and compared using ncbi’s cn3d []., phamerator [] was used to analyze the differentiating features between jenst and sectim467. the palindrome command of emboss [] was used to verify […]

2015
PMCID: 4287437
PMID: 25569504
DOI: 10.1371/journal.pcbi.1004021

[…] crystal structures of ph domains were obtained from pdb, and we curated 34 non-redundant proteins. their pdb ids are listed in . they were used for secondary structure-based sequence alignment with strap . we extracted the multiple sequence alignments for β1, β2, β3, β6, β7 and α1 secondary structural fragments. the individual alignment will be used as input to psi-blast which could generate […]

2014
PMCID: 4223420
PMID: 25023829
DOI: 10.1186/1756-3305-7-330

[…] weight and isoelectric points of the mature serpin protein were calculated using the expasy compute pi/mw tool []., the sjb6 amino acid sequence was subjected to structural based alignment using strap [] and the muscle algorithm []. the tertiary structures of sjb6 and other parasitic helminth serpins were predicted using the phyre2 program []. qmean was the method used to estimate model […]

2012
PMCID: 3475032
PMID: 22862831
DOI: 10.1186/1756-0500-5-410

[…] bank) []. pair wise analysis of structures was done using dalilite []. analysis of active site residues was done with the spdbv (swiss pdb viewer), alignments and cladograms were generated with the strap suite of programs (structural alignment of proteins), and hmmer 3.0 was used for model building, analysis, database construction, and similarity studies with user defined input sequences [-]. […]

2010
PMCID: 2816704
PMID: 20140205
DOI: 10.1371/journal.pone.0009071

[…] was aligned pair-wise with the crystal structures of cole9 (pdb: 1v14), i-hmui (pdb: 1u3e), hpy99i (pdb: 3gox) and the kpni model built by nagaraja and colleagues using the tm-align module of strap ., we thank rich roberts, bill jack, and elisabeth raleigh for critical comments and discussions; barry stoddard for informing us of the hpyav homologs; jim ellard and don comb for support […]


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STRAP in publications

 (19)
PMCID: 5686155
PMID: 29138502
DOI: 10.1038/s41467-017-01701-2

[…] (schrödinger, llc). docking of lipoyl-lys in the xsirt4/adpr active-site was done with leadit (biosolveit gmbh, sankt augustin, germany)., structure-based sequence alignments were created using strap with the integrated aligner3d algorithm, and manual editing and phylogenetic tree generation were done with bioedit. conservation levels were mapped on the xsirt4 structure surface using […]

PMCID: 5014327
PMID: 27603010
DOI: 10.1371/journal.pone.0162165

[…] 2cjp.a), served as the model-building template (alignment length 335 amino acids, double-sided z-score 28.6). the catalytic triad of cld1p (h424, d392, s230) was originally identified using strap [], which facilitated the structure-guided alignment of several hundred α/β hydrolase fold-containing proteins, and the authenticity of this triad has now been confirmed experimentally []., […]

PMCID: 4909266
PMID: 27304881
DOI: 10.1371/journal.pone.0156838

[…] serovar typhimurium) [1adr_a, 2r1j_l, 3jxb_c] []. hhpred [] and raptorx [–] were used to predict tertiary structure and binding sites. these predicted structures were then superimposed using strap [] and compared using ncbi’s cn3d []., phamerator [] was used to analyze the differentiating features between jenst and sectim467. the palindrome command of emboss [] was used to verify […]

PMCID: 4727276
PMID: 26810894
DOI: 10.1186/s13062-016-0106-9

[…] are most successful in case there is a similarity between the query and experimentally annotated proteins [, ]. following are few examples of similarity-based methods and databases; confunc, pfp, strap, prsf, blast2go, cdd, prosite, pfam, smart, prodom [–]. in summary, homology-based methods are imperative in the present era as known proteins (experimentally characterize data) are growing […]

PMCID: 4630614
PMID: 26525192
DOI: 10.1038/srep16056

[…] the ccp4 program suite. statistics from the data collection and structure refinement are summarized in . structural comparison and structure-based sequence alignment were performed using the program strap. all figures representing the ubca1 structure were generated using the molecular visualization program pymol., three single or double site-directed mutants, k122p, k124p and k122p/k124p, […]


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STRAP institution(s)
Institute for Biochemistry, Charité University Hospital, Humboldt University Berlin, Germany

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