Scalable web services for the PSIPRED Protein Analysis Workbench
TLDR
The PSIPRED Protein Analysis Workbench unites all of the previously available analysis methods into a single web-based framework and provides a greatly streamlined user interface with a number of new features to allow users to better explore their results.Abstract:
Here, we present the new UCL Bioinformatics Group’s PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.read more
Citations
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Journal ArticleDOI
The PSIPRED Protein Analysis Workbench: 20 years on.
TL;DR: The work to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 years is presented and updates to some of the key predictive algorithms available through the website are surveyed.
Journal ArticleDOI
Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction.
Yimin Shen,Yimin Shen,Julien Maupetit,Julien Maupetit,Philippe Derreumaux,Philippe Derreumaux,Philippe Derreumaux,Pierre Tufféry,Pierre Tufféry +8 more
TL;DR: The results indicate that if the coarse-grained PEP-FOLD2 method is approaching maturity, the authors are not at the end of the game of mini-protein structure prediction, but this opens new perspectives for large-scale in silico experiments.
Journal ArticleDOI
Integrative structure and functional anatomy of a nuclear pore complex
Seung Joong Kim,Javier Fernandez-Martinez,Ilona Nudelman,Yi Shi,Wenzhu Zhang,Barak Raveh,Thurston Herricks,Brian D. Slaughter,Joanna A. Hogan,Paula Upla,Ilan E. Chemmama,Riccardo Pellarin,Ignacia Echeverria,Manjunatha Shivaraju,Azraa S. Chaudhury,Junjie Wang,Rosemary Williams,Jay R. Unruh,Charles H. Greenberg,Erica Y. Jacobs,Zhiheng Yu,M. Jason de la Cruz,Roxana Mironska,David L. Stokes,John D. Aitchison,John D. Aitchison,Martin F. Jarrold,Jennifer L. Gerton,Steven J. Ludtke,Christopher W. Akey,Brian T. Chait,Andrej Sali,Michael P. Rout +32 more
TL;DR: The structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae is determined at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents.
Journal ArticleDOI
The architecture of respiratory supercomplexes
TL;DR: These are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain of mammalian (ovine) supercomplexes determined by cryo-electron microscopy.
Journal ArticleDOI
Cryo-EM Structure of the Open Human Ether-a-go-go-Related K(+) Channel hERG.
Weiwei Wang,Roderick MacKinnon +1 more
TL;DR: The molecular structure of hERG is determined to 3.8 Å using cryo-electron microscopy, and the central cavity has an atypically small central volume surrounded by four deep hydrophobic pockets, which may explain hERG's unusual sensitivity to many drugs.
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