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Automated protein function prediction--the genomic challenge

I. Friedberg
2006 Briefings in Bioinformatics  
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

Baohong Zhang, Leszek Rychlewski, Krzysztof Pawlowski, Jacquelyn S. Fetrow, Jeffrey Skolnick, Adam Godzik
1999 Protein Science  
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

Kai Wang, Ram Samudrala
2006 BMC Bioinformatics  
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

Yang Zhang
2009 Proteins: Structure, Function, and Bioinformatics  
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

Ishita K. Khan, Qing Wei, Meghana Chitale, Daisuke Kihara
2014 Computer applications in the biosciences : CABIOS  
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

Ahmet Sureyya Rifaioglu, Tunca Doğan, Maria Jesus Martin, Rengul Cetin-Atalay, Volkan Atalay
2019 Scientific Reports  
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

Dylan Chivian, David E. Kim, Lars Malmström, Jack Schonbrun, Carol A. Rohl, David Baker
2005 Proteins: Structure, Function, and Bioinformatics  
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

Daniel Fischer, Arne Elofsson, Leszek Rychlewski, Florencio Pazos, Alfonso Valencia, Burkhard Rost, Angel R. Ortiz, Roland L. Dunbrack
2001 Proteins: Structure, Function, and Bioinformatics  
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

Daniel Fischer, Leszek Rychlewski, Roland L. Dunbrack, Angel R. Ortiz, Arne Elofsson
2003 Proteins: Structure, Function, and Bioinformatics  
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

Dylan Chivian, David E. Kim, Lars Malmstr�m, Philip Bradley, Timothy Robertson, Paul Murphy, Charles E.M. Strauss, Richard Bonneau, Carol A. Rohl, David Baker
2003 Proteins: Structure, Function, and Bioinformatics  
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

J. Zhou, J. H. Miller
2002 Journal of Bacteriology  
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

Alfonso Valencia, Manuel Hidalgo
2012 Genome Medicine  
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

Philip Bradley, Dylan Chivian, Jens Meiler, Kira M.S. Misura, Carol A. Rohl, William R. Schief, William J. Wedemeyer, Ora Schueler-Furman, Paul Murphy, Jack Schonbrun, Charles E.M. Strauss, David Baker
2003 Proteins: Structure, Function, and Bioinformatics  
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

C. J. Hack
2004 Briefings in Functional Genomics & Proteomics  
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

Urmila Kulkarni-Kale, Shriram G Bhosle, G Sunitha Manjari, Manali Joshi, Sandeep Bansode, Ashok S Kolaskar
2006 BMC Bioinformatics  
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
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