ENDscript protocols

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ENDscript specifications

Information


Unique identifier OMICS_03823
Name ENDscript
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline ENDscript Team <>

Publication for ENDscript

ENDscript in pipeline

2016
PMCID: 4965698
PMID: 27540468
DOI: 10.5256/f1000research.9528.r14191

[…] for positively charged residues, medium blue for negatively charged residues and light blue for amides., multiple sequence alignment was done using mafft (v7.123b) , and figures generated using the endscript server . in order to obtain a multiple sequence alignment with a single representative of a stereochemical group (positive, negative, aromatic and non-polar residues) the following […]


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ENDscript in publications

 (24)
PMCID: 5942844
PMID: 29702654
DOI: 10.1371/journal.pntd.0006428

[…] 7 [] multiple sequence comparison by log-expectation (muscle []) and clustal w [] respectively. the phylogenetic trees were using the neighbor-joining method []. the results were displayed using endscript (http://endscript.ibcp.fr/) []. accession numbers for sequences included can be found in the material & methods section., for the construction of a phylogenetic tree () covering […]

PMCID: 5793182
PMID: 29324689
DOI: 10.3390/genes9010030

[…] minimization were also performed for the refinement of structures. secondary structures assignments and relative solvent accessibility (rsa) were calculated by the dssp program [,] as implemented in endscript []. additionally, consurf webserver [] was used to map the evolutionary variability of amino acids onto the reconstructed structures of homologues which were rendered using the ucsf chimera […]

PMCID: 5755878
PMID: 29304092
DOI: 10.1371/journal.pone.0190618

[…] were submitted to a multiple sequence alignment at the clustal omega server (http://www.ebi.ac.uk/tools/services/web_clustalo/toolform.ebi) and their secondary structures were generated using the endscript/espript 3.0 server []. additionally, both dpp3 sequences were submitted to the phyre 2 server [] to obtain their 3d structure models. in the case of hdpp3, the model constructed […]

PMCID: 5725463
PMID: 29229913
DOI: 10.1038/s41598-017-16839-8

[…] (version 30) and the hmmer program (version 3.1) were used to generate sequence alignments of engu with selected pfam families. secondary structure-based alignments were performed with t-coffee and endscript., the dna fragments encoding engu were amplified by pcr with pfu dna polymerase (thermofisher scientific) or with q5 polymerase (new england biolabs) according to the manufacturer’s […]

PMCID: 5697364
PMID: 29157307
DOI: 10.1186/s13071-017-2523-8

[…] parts of the four models. in addition, potential errors in the 3d models were evaluated using a ramachandran plot [] and errat []., structural conservation was calculated and visualized using endscript/espript v. 3.0 [] with the pdbaa95 database, e-value of 1e-12, and contact range of 2.7 å. coach [] was used to predict ligand-binding sites in csmrp4. sdf files for bile acids […]


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ENDscript institution(s)
Equipe de Biocristallographie et Biologie Structurale des Cibles Thérapeutiques, IBCP-BMSSI, UMR 5086 CNRS Université de Lyon, SFR BioSciences Gerland-Lyon Sud, Lyon, France

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