A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2010; you can also visit the original URL.
The file type is application/pdf.
Filters
Automated protein function prediction--the genomic challenge
2006
Briefings in Bioinformatics
Preserved Fulltext
This article briefly outlines the history of automated protein function prediction and surveys the latest innovations in all three topics. ...
Again, the subjectivity of the term 'function' and the various aspects of biological function make this a challenging effort. ...
This study was supported by the National Institutes of Health grant 1P01-GM63208. ...
doi:10.1093/bib/bbl004
pmid:16772267
fatcat:br64i2dpcfeq7nmyqpfez4ru3q
From fold predictions to function predictions: Automation of functional site conservation analysis for functional genome predictions
1999
Protein Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
An automated assessment of function conservation is used to analyze the relation between fold and function similarity for a large number of fold predictions. ...
Over 100 new fold0function predictions in this class were obtained in the E. coli genome. ...
and is likely to challenge many existing functional assignments in genomic databases. ...
doi:10.1110/ps.8.5.1104
pmid:10338021
pmcid:PMC2144342
fatcat:iagnwhpgvzgati5qvwwb7vxooi
Automated functional classification of experimental and predicted protein structures
2006
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Conclusion: The results indicate that the FSSA algorithm has better accuracy when compared to homology-based approaches for functional classification of both experimental and predicted protein structures ...
time, when the protein is a member of a multi-functional fold family. ...
Additional File 1 Comparative evaluation of three prediction methods (FSSA, MAM-MOTH and SSEARCH) on selected prediction targets from the LiveBench 7, LiveBench 8, LiveBench 9 and PDB-CAFASP 1 experiments ...
doi:10.1186/1471-2105-7-278
pmid:16749925
pmcid:PMC1513613
fatcat:bmry6lik65b3fm2icfjqog5n7e
I-TASSER: Fully automated protein structure prediction in CASP8
2009
Proteins: Structure, Function, and Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
7-9 Undoubtedly, with the rapid accumulation of genome-wide sequences, the development of fully automated computer-based structure prediction methods becomes unprecedentedly demanded. 10 human predictors ...
INTRODUCTION When will computers beat humans in protein structure prediction? Or are there still any human insights that cannot be reproduced in automated approaches? ...
ACKNOWLEDGMENTS The author thanks Drs. S. Wu, Y. Li, and A. Roy for assistance in CASP8, Dr. A. Szilagyi for reading the manuscript. ...
doi:10.1002/prot.22588
pmid:19768687
pmcid:PMC2782770
fatcat:wwdfvn4c3vee7kbzovoum2xmru
PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool
2014
Computer applications in the biosciences : CABIOS
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2016; you can also visit the original URL.
The file type is application/pdf.
Protein function prediction (PFP) is an automated function prediction method that predicts Gene Ontology (GO) annotations for a protein sequence using distantly related sequences and contextual associations ...
Here, we provide interactive web servers for the PFP and ESG algorithms that are equipped with an effective visualization of the GO predictions in a hierarchical topology. ...
SUMMARY Web servers of two sequence-based function prediction methods, PFP and ESG, are developed. ...
doi:10.1093/bioinformatics/btu646
pmid:25273111
pmcid:PMC4287954
fatcat:rzx5k2uvtjabjpwl2l3fwnqd7e
DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks
2019
Scientific Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Automated protein function prediction is critical for the annotation of uncharacterized protein sequences, where accurate prediction methods are still required. ...
The overall predictive performance of DEEPred was assessed using CAFA2 and CAFA3 challenge datasets, in comparison with the state-of-the-art protein function prediction methods. ...
Acknowledgements The authors would like to thank Andrew Nightingale for the critical reading of the manuscript. ASR was supported by YOK OYP scholarship. ...
doi:10.1038/s41598-019-43708-3
pmid:31089211
pmcid:PMC6517386
fatcat:7ayut2gfubfojhw74posmhrvbq
Prediction of CASP6 structures using automated robetta protocols
2005
Proteins: Structure, Function, and Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2007; you can also visit the original URL.
The file type is application/pdf.
Robetta is a publicly available protein structure prediction server (http://robetta.bakerlab.org/) that uses the Rosetta de novo structure prediction method. ...
We find that the Robetta server shows the greatest promise for the more challenging targets.The most significant finding from CASP-5, that automated protocols can be roughly comparable in ability with ...
INTRODUCTION Full automation of protein structure prediction is a desirable goal as it opens the door to genome-level protein structure modeling and, equally importantly, provides a stringent test of the ...
doi:10.1002/prot.20733
pmid:16187358
fatcat:e2zaiwkyl5azddsuisbdq2dyrq
CAFASP2: The second critical assessment of fully automated structure prediction methods
2001
Proteins: Structure, Function, and Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2010; you can also visit the original URL.
The file type is application/pdf.
Proteins 2001;Suppl 5:171-183. ...
The results of the second Critical Assessment of Fully Automated Structure Prediction (CAFASP2) are presented. ...
The utility of structural genomics will be achieved only if automated, reliable tools succeed to model most of the proteins closely and distantly related to proteins of known structures. ...
doi:10.1002/prot.10036
pmid:11835495
fatcat:llmxmpcec5f7vfwatkyyqb2chi
CAFASP3: The third critical assessment of fully automated structure prediction methods
2003
Proteins: Structure, Function, and Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2006; you can also visit the original URL.
The file type is application/pdf.
genomics. ...
Proteins 2003;53:503-516. ...
Only if automated, reliable tools are able to model most of the proteins closely and distantly related to CAFASP3 proteins of known structures will the goals of structural genomics be achieved. ...
doi:10.1002/prot.10538
pmid:14579340
fatcat:5rn7xf2sxnbm3lm4dpu7i2qrcy
Automated prediction of CASP-5 structures using the Robetta server
2003
Proteins: Structure, Function, and Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Robetta is a fully automated protein structure prediction server that uses the Rosetta fragment-insertion method. ...
The Robetta server produced some reasonable predictions for targets in the recent CASP-5 and CAFASP-3 experiments. ...
Karplus for the use of the SAM-T99 software, David Jones for the use of the PSIPRED software, Jens Meiler for the use of the JUFO ...
doi:10.1002/prot.10529
pmid:14579342
fatcat:ivsfr77knrck5jo2eep7udsq54
Microbial Genomics--Challenges and Opportunities: The 9th International Conference on Microbial Genomes
2002
Journal of Bacteriology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
ACKNOWLEDGMENTS We gratefully acknowledge the support of the DOE, the NSF, the U.S. Department of Agriculture, New England BioLabs, DuPont Life Sciences, and Oak Ridge National Laboratory. ...
We especially thank the We thank Michael Adams and Dorothea K. Thompson for critically reading this meeting review. ...
To address the challenges of functional genomics, the DOE Office of Science has launched various microbial genomics-related research programs, such as the Microbial Genome Program (www.ornl.gov /microbialgenomes ...
doi:10.1128/jb.184.16.4327-4333.2002
pmid:12142401
pmcid:PMC135260
fatcat:rfuemw6jmrcvjnn3vmrkl7avd4
Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics
2012
Genome Medicine
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
The assistance provided by the Spanish Bioinformatics Institute (INB), a platform of the ISCII, is particularly appreciated. ...
Acknowledgements The work in the group of AV related to this review is supported by grants from the ENCODE Project (U54 HG0004555), eTOX (Grant 115002, Innovative Medicines Initiative) and Consolider E-Science ...
[88, 89] , CASP for predicting function and binding sites [90] , and challenge in function prediction organized by Iddo Friedberg and Predrag Radivojac [91] . ...
doi:10.1186/gm362
pmid:22839973
pmcid:PMC3580417
fatcat:2t5baj5uovdw7p72ohvorkufdy
Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation
2003
Proteins: Structure, Function, and Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
A fully automated version of the CASP5 protocol produced results that were comparable to the human-assisted predictions for most of the targets, suggesting that automated genomic-scale, de novo protein ...
For the three targets where the human-assisted predictions were significantly closer to the native structure, we identify the steps that remain to be automated. Proteins 2003;53:457-468. ...
ACKNOWLEDGMENTS The authors thanks the CASP5 organizers and assessors, the experimentalists who participated in CASP5, and Nick Grishin and Ming Tang for analysis of the full Rosetta decoy sets. ...
doi:10.1002/prot.10552
pmid:14579334
fatcat:jo2rfynasbcfpoewaxcy7hiaqe
Integrated transcriptome and proteome data: The challenges ahead
2004
Briefings in Functional Genomics & Proteomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2006; you can also visit the original URL.
The file type is application/pdf.
and a member of the Bioinformatics Research Group. ...
Acknowledgments I am indebted to colleagues at GlaxoSmithKline, King of Prussia, PA -in particular Bill Reisdorf and Pankaj Agawal -for inspiring discussions during the initial stages of this study. ...
has indicated the prevalence of comigrating proteins, while proteins predicted from genome sequences have helped identify many categories of proteins which were under-represented in results from gels. ...
doi:10.1093/bfgp/3.3.212
pmid:15642185
fatcat:hayszxgxhvcrzacyj5iz3vgpfu
Curation of viral genomes: challenges, applications and the way forward
2006
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
One of the approaches to achieve this goal is to carry out functional annotations using comparative genomics. ...
One of the unique features of VirGen is predicted conformational and sequential epitopes of known antigenic proteins using in-house developed algorithms, a step towards reverse vaccinology. ...
The authors would like to thank the anonymous reviewers for their useful suggestions to improve the presentation of this manuscript. ...
doi:10.1186/1471-2105-7-s5-s12
pmid:17254296
pmcid:PMC1764468
fatcat:635j62y6xzgr3nhfeap4ea5rom
« Previous
Showing results 1 — 15 out of 47,866 results