The PSIPRED Protein Analysis Workbench: 20 years on

By Daniel W. A. Buchan, David T. Jones. 2019

1,212 citations recorded by the source corpus.

Abstract The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 years. The main focus of our recent website upgrade work has been the acceleration of analyses in the face of increasing protein sequence database size. We additionally discuss any new software, the new hardware infrastructure, our webservices and web site. Lastly we survey updates to some of the key predictive algorithms available through our website.

Subfields: Molecular Biology, Spectroscopy

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Spectroscopy

Citations in the corpus

Protein sequence design with a learned potential (2022, methodology): “Native test case runs used Psipred predictions from MSA features after UniRef90 69 database alignment.”
Protein sequence design with a learned potential (2020, background): “To confirm that key sequence features are retained despite the increased variability seen, we calculated Psipred [94, 95, 96, 97, 98, 99] secondary structure prediction accuracy relative to DSSP assignments [100] and found that the predictions for model-designed sequences from single sequences alone”
A guide to machine learning for biologists (2021, background): “Fixed number of features Protein secondary structure prediction [13]”
Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan (2020, methodology): “For the prediction of protein secondary structure including beta sheet, alpha helix, and coil, initial amino acid sequences were input and analysed using neural networking and its own algorithm.”
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type (2019, methodology): “Prediction of 3-state secondary structures (helix, strand, and coil) were made by three programs (PSIPRED [94], SPIDER [95], and PSSpred [96]), resulting in nine features.”
Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes (2022, methodology): “The secondary structure and coiled-coil regions were predicted using PsiPred 55 , Jpred 56 , and Marcoil 57 , Deepcoil 58 and Pcoils 59,60 .”