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Protocols

ESPript specifications

Information


Unique identifier OMICS_21153
Name ESPript
Alternative name Easy Sequencing in PostScript
Interface Web user interface
Restrictions to use None
Input data Some pre-aligned sequences and a list of secondary structures.
Output data A colourful PostScript file.
Programming languages Fortran
Computer skills Basic
Version 3.0
Maintained Yes

Documentation


Maintainers


  • person_outline ENDscript Team
  • person_outline Patrice Gouet

Additional information


http://espript.ibcp.fr/ESPript/ESPript/esp_userguide.php http://imed.med.ucm.es/ESPript/cgi-bin/ESPript.cgi

Publication for Easy Sequencing in PostScript

ESPript citations

 (248)
call_split

A plasmid borne, functionally novel glycoside hydrolase family 30 subfamily 8 endoxylanase from solventogenic Clostridium

2018
PMCID: 5934979
PMID: 29626157
DOI: 10.1042/BCJ20180050
call_split See protocol

[…] /fasta_www.cgi?rm=shuffle) of the FASTA online package available through the University of Virginia (http://fasta.bioch.virginia.edu/fasta/fasta_list.html). Alignment figures were generated using the ESPript web server [] available at http://espript.ibcp.fr/ESPript/ESPript/index.php. The studies involved in this work rely on the continued maintenance of the CAZy Database (http://www.cazy.org/) [] […]

library_books

Various Bee Pheromones Binding Affinity, Exclusive Chemosensillar Localization, and Key Amino Acid Sites Reveal the Distinctive Characteristics of Odorant Binding Protein 11 in the Eastern Honey Bee, Apis cerana

2018
Front Physiol
PMCID: 5924804
PMID: 29740337
DOI: 10.3389/fphys.2018.00422

[…] ignalP/) (Petersen et al., ). OBPs protein alignments were made using ClustalX V1.83 (Thompson et al., ) with default gap penalty parameters of gap opening 10 and extension 0.2, and were edited using ESPript (http://espript.ibcp.fr/ESPript/ESPript/) (Robert and Gouet, ). Phylogenetic tree was constructed by the neighbor joining method using MEGA V6.0 (http://www.megasoftware.net/) (Tamura et al., […]

call_split

CD22 Binding Synthetic Sialosides Regulate B Lymphocyte Proliferation Through CD22 Ligand Dependent and Independent Pathways, and Enhance Antibody Production in Mice

2018
Front Immunol
PMCID: 5917077
PMID: 29725338
DOI: 10.3389/fimmu.2018.00820
call_split See protocol

[…] ing the coordinates of the ligand-binding domain of human CD22 () (PDB ID 5VKM, residues 20–138) as a template structure. The figures of the sequence alignment and molecular models are prepared using ESPript () and PyMOL (The PyMOL Molecular Graphics System, Schrödinger, LLC.), respectively. […]

library_books

Molecular Characterization, Evolution, and Expression Profiling of the Dirigent (DIR) Family Genes in Chinese White Pear (Pyrus bretschneideri)

2018
Front Genet
PMCID: 5911567
PMID: 29713336
DOI: 10.3389/fgene.2018.00136

[…] A5.1 software (). The gene sequence information used to construct the phylogenetic tree is listed in Supplementary Table . The secondary and three-dimensional structures of proteins were predicted by Espript3.0 and Protein Fold Recognition Server, respectively. […]

library_books

An Evolutionarily Conserved Mechanism for Intrinsic and Transferable Polymyxin Resistance

2018
MBio
PMCID: 5893884
PMID: 29636432
DOI: 10.1128/mBio.02317-17

[…] Sequence alignment of PEA lipid A transferases was conducted with Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/) and processed via the program ESPript 3.0 (http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi) (). The transmembrane regions of EptA and MCR-1 and -2 were predicted using TMHMM server version 2.0 (http://www.cbs.dtu.dk/services/TM […]

library_books

Mechanism of Apoptosis Induction by Mycoplasmal Nuclease MGA_0676 in Chicken Embryo Fibroblasts

2018
PMCID: 5893762
PMID: 29670864
DOI: 10.3389/fcimb.2018.00105

[…] cleavage sites in MGA_0676 was performed using SignalP Server (http://www.cbs.dtu.dk/services/SignalP/). Sequence alignment analysis and three-dimensional (3D) structure modeling were performed using ESPript 2.2 (http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi) and homology remodeling tools (http://swissmodel.expasy.org/workspace/index). Prediction of the interactions between proteins was done […]

Citations

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ESPript institution(s)
Laboratory of Molecular Biophysics, Oxford, UK; Groupe de Cristallographie Biologique, lnstitut de Pharmacologie et de Biologie Structurale, Toulouse, France; Oxford Centre for Molecular Sciences, Oxford, UK; lnstitut de Biologie Structurale, Grenoble, France

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