ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.
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TLDR
The quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer in the ProSA-web service.Abstract:
A major problem in structural biology is the recognition of errors in experimental and theoretical models of protein structures. The ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. The analysis of protein structures is generally a difficult and cumbersome exercise. The new service presented here is a straightforward and easy to use extension of the classic ProSA program which exploits the advantages of interactive web-based applications for the display of scores and energy plots that highlight potential problems spotted in protein structures. In particular, the quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. The service specifically addresses the needs encountered in the validation of protein structures obtained from X-ray analysis, NMR spectroscopy and theoretical calculations. ProSA-web is accessible at https://prosa.services.came.sbg.ac.at.read more
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Journal ArticleDOI
Comparative Protein Structure Modeling Using MODELLER
Narayanan Eswar,Ben Webb,Marc A. Marti-Renom,Mallur S. Madhusudhan,David Eramian,Min-Yi Shen,Ursula Pieper,Andrej Sali +7 more
TL;DR: This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications.
Journal ArticleDOI
Comparative protein structure modeling using Modeller.
Narayanan Eswar,Ben Webb,Marc A. Marti-Renom,Mallur S. Madhusudhan,David Eramian,Min-Yi Shen,Ursula Pieper,Andrej Sali +7 more
TL;DR: This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications.
Journal ArticleDOI
Toward the estimation of the absolute quality of individual protein structure models
TL;DR: The ability of the newly introduced QMEAN Z-score to detect experimentally solved protein structures containing significant errors, as well as to evaluate theoretical protein models is demonstrated.
Journal ArticleDOI
SHIFTX2: significantly improved protein chemical shift prediction
TL;DR: A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data and will open the door to many long-anticipated applications of chemical shift prediction to protein structure determination, refinement and validation.
Journal ArticleDOI
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
Simon Roux,Jennifer R. Brum,Bas E. Dutilh,Bas E. Dutilh,Bas E. Dutilh,Shinichi Sunagawa,Melissa B. Duhaime,Alexander Loy,Bonnie T. Poulos,Natalie Solonenko,Elena Lara,Elena Lara,Julie Poulain,Stephane Pesant,Stefanie Kandels-Lewis,Céline Dimier,Céline Dimier,Céline Dimier,Marc Picheral,Marc Picheral,Sarah Searson,Sarah Searson,Corinne Cruaud,Adriana Alberti,Carlos M. Duarte,Carlos M. Duarte,Josep M. Gasol,Dolors Vaqué,Peer Bork,Silvia G. Acinas,Patrick Wincker,Patrick Wincker,Mathew B. Sullivan +32 more
TL;DR: A global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts is presented to present a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.
References
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