title: Deciphering key features in protein structures with the new ENDscript server.
abstract: ENDscript 2 is a friendly Web server for extracting and rendering a comprehensive analysis of primary to quaternary protein structure information in an automated way. This major upgrade has been fully re-engineered to enhance speed, accuracy and usability with interactive 3D visualization. It takes advantage of the new version 3 of ESPript, our well-known sequence alignment renderer, improved to handle a large number of data with reduced computation time. From a single PDB entry or file, ENDscript produces high quality figures displaying multiple sequence alignment of proteins homologous to the query, colored according to residue conservation. Furthermore, the experimental secondary structure elements and a detailed set of relevant biophysical and structural data are depicted. All this information and more are now mapped on interactive 3D PyMOL representations. Thanks to its adaptive and rigorous algorithm, beginner to expert users can modify settings to fine-tune ENDscript to their needs. ENDscript has also been upgraded as an open platform for the visualization of multiple biochemical and structural data coming from external biotool Web servers, with both 2D and 3D representations. ENDscript 2 and ESPript 3 are freely available at http://endscript.ibcp.fr and http://espript.ibcp.fr, respectively.
authors.affiliation: Equipe de Biocristallographie et Biologie Structurale des Cibles Thérapeutiques, IBCP-BMSSI, UMR 5086 CNRS Université de Lyon, SFR BioSciences Gerland-Lyon Sud, 7 Passage du Vercors, 69367 Lyon Cedex 07, France patrice.gouet@ibcp.fr.
authors.forename: Xavier
authors.initials: X
authors.lastname: Robert
authors.affiliation: Equipe de Biocristallographie et Biologie Structurale des Cibles Thérapeutiques, IBCP-BMSSI, UMR 5086 CNRS Université de Lyon, SFR BioSciences Gerland-Lyon Sud, 7 Passage du Vercors, 69367 Lyon Cedex 07, France patrice.gouet@ibcp.fr.
authors.forename: Patrice
authors.initials: P
authors.lastname: Gouet
mesh_terms: D000465:Algorithms; D002374:Catalase / Q000737:chemistry; D020407:Internet; D011487:Protein Conformation; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D002374:Catalase
references.citation: Nucleic Acids Res. 1988 Nov 25;16(22):10881-90
references.pmid: 2849754
references.citation: Mol Syst Biol. 2011 Oct 11;7:539
references.pmid: 21988835
references.citation: Mol Biol Evol. 2013 Apr;30(4):772-80
references.pmid: 23329690
references.citation: Protein Eng. 1993 Jan;6(1):37-40
references.pmid: 8433969
references.citation: Trends Biochem Sci. 2000 Mar;25(3):147-50
references.pmid: 10694887
references.citation: Acta Crystallogr D Biol Crystallogr. 2002 Jun;58(Pt 6  No 1):899-907
references.pmid: 12037327
references.citation: Biochim Biophys Acta. 1995 Sep 27;1252(1):172-6
references.pmid: 7548161
references.citation: Bioinformatics. 2009 May 1;25(9):1189-91
references.pmid: 19151095
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D8-D20
references.pmid: 23193264
references.citation: Methods Mol Biol. 2014;1079:75-101
references.pmid: 24170396
references.citation: Bioinformatics. 2001 Apr;17(4):377-8
references.pmid: 11301311
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D212-5
references.pmid: 15608179
references.citation: Methods Mol Biol. 2014;1079:211-8
references.pmid: 24170405
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W289-94
references.pmid: 15980472
references.citation: Bioinformatics. 2002 May;18(5):767-8
references.pmid: 12050076
references.citation: Bioinformatics. 1999 Apr;15(4):305-8
references.pmid: 10320398
references.citation: J Mol Biol. 1995 Jun 23;249(5):933-54
references.pmid: 7791219
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3320-3
references.pmid: 12824317
references.citation: Methods Mol Biol. 2014;1079:263-71
references.pmid: 24170408
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7
references.pmid: 21558174
references.citation: Acta Crystallogr D Biol Crystallogr. 2009 May;65(Pt 5):510-2
references.pmid: 19390156
references.citation: BMC Bioinformatics. 2009 Dec 15;10:421
references.pmid: 20003500