The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

/pdf/ucsf-chimera-a-visualization-system-for-exploratory-research-59xu54fhxg.pdf

UCSF Chimera--a visualization system for exploratory research and analysis.

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.

/pdf/deciphering-key-features-in-protein-structures-with-the-new-3kiylhufbn.pdf

Deciphering key features in protein structures with the new ENDscript server

▪ Abstract Most prokaryotic signal-transduction systems and a few eukaryotic pathways use phosphotransfer schemes involving two conserved components, a histidine protein kinase and a response regul...

Two-component signal transduction

http://hub.hku.hk/bitstream/10722/289788/1/content.pdf

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited.Thislicensedoesnot permit commercial exploitation or the creation of derivative works without specific permission.

MOTIVATION: The program ESPript (Easy Sequencing in PostScript) allows the rapid visualization, via PostScript output, of sequences aligned with popular programs such as CLUSTAL-W or GCG PILEUP It can read secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information RESULTS: ESPript can be run via a command file or a friendly html-based user interface The program calculates an homology score by columns of residues and can sort this calculation by groups of sequences It offers a palette of markers to highlight important regions in the alignment ESPript can also paste information on residue conservation into coordinate files, for subsequent visualization with a graphics program AVAILABILITY: ESPript can be accessed on its Web site at http://wwwipbsfr/ESPript Sources and helpfiles can be downloaded via anonymous ftp from ftpipbsfr A tar file is held in the directory pub/ESPriptMOTIVATION: The program ESPript (Easy Sequencing in PostScript) allows the rapid visualization, via PostScript output, of sequences aligned with popular programs such as CLUSTAL-W or GCG PILEUP It can read secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information RESULTS: ESPript can be run via a command file or a friendly html-based user interface The program calculates an homology score by columns of residues and can sort this calculation by groups of sequences It offers a palette of markers to highlight important regions in the alignment ESPript can also paste information on residue conservation into coordinate files, for subsequent visualization with a graphics program AVAILABILITY: ESPript can be accessed on its Web site at http://wwwipbsfr/ESPript Sources and helpfiles can be downloaded via anonymous ftp from ftpipbsfr A tar file is held in the directory pub/ESPript

/pdf/espript-analysis-of-multiple-sequence-alignments-in-1ga2w94jy8.pdf

ESPript: Analysis of multiple sequence alignments in PostScript

The fortran program ESPript was created in 1993, to display on a PostScript figure multiple sequence alignments adorned with secondary structure elements. A web server was made available in 1999 and ESPript has been linked to three major web tools: ProDom which identifies protein domains, PredictProtein which predicts secondary structure elements and NPS@ which runs sequence alignment programs. A web server named ENDscript was created in 2002 to facilitate the generation of ESPript figures containing a large amount of information. ENDscript uses programs such as BLAST, Clustal and PHYLODENDRON to work on protein sequences and such as DSSP, CNS and MOLSCRIPT to work on protein coordinates. It enables the creation, from a single Protein Data Bank identifier, of a multiple sequence alignment figure adorned with secondary structure elements of each sequence of known 3D structure. Similar 3D structures are superimposed in turn with the program PROFIT and a final figure is drawn with BOBSCRIPT, which shows sequence and structure conservation along the Cα trace of the query. ESPript and ENDscript are available at http://genopole.toulouse.inra.fr/ESPript.

ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins

The structure of the core of bluetongue virus has been determined at 3.5 resolution, revealing molecular details of mismatched symmetry. This is the largest structure yet determined by X-ray crystallography.

The atomic structure of bluetongue virus core

The structure of the core particle of bluetongue virus has been determined by X-ray crystallography at a resolution approaching 3.5 A. This transcriptionally active compartment, 700 A in diameter, represents the largest molecular structure determined in such detail. The atomic structure indicates how approximately 1,000 protein components self-assemble, using both the classical mechanism of quasi-equivalent contacts, which are achieved through triangulation, and a different method, which we term geometrical quasi-equivalence.

Patrice Gouet

Papers

Deciphering key features in protein structures with the new ENDscript server

ESPript: Analysis of multiple sequence alignments in PostScript

ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins

The atomic structure of bluetongue virus core

The atomic structure of the bluetongue virus core