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EVA: continuous automatic evaluation of protein structure prediction servers

V. A. Eyrich, M. A. Marti-Renom, D. Przybylski, M. S. Madhusudhan, A. Fiser, F. Pazos, A. Valencia, A. Sali, B. Rost
2001 Bioinformatics  
Here, we describe EVA, a web server for assessing protein structure prediction methods, in an automated, continuous and large-scale fashion.  ...  Currently, EVA evaluates four different categories of structure prediction servers (see EVA home page for URLs and list of servers evaluated): comparative modelling (3 servers), threading (6 servers),  ...  We also like to thank Arne Elofsson ( We apologise to all whose servers we evaluated that we had to remove their citations from this paper; they can be found at: http://cubic.bioc.columbia.edu/eva/doc  ... 
doi:10.1093/bioinformatics/17.12.1242 pmid:11751240 fatcat:r2hjvhewdvfltcqzsebrgarxsy

EVA: evaluation of protein structure prediction servers

I. Y. Y. Koh
2003 Nucleic Acids Research  
EVA (http://cubic.bioc.columbia.edu/eva/) is a web server for evaluation of the accuracy of automated protein structure prediction methods.  ...  The evaluation is updated automatically each week, to cope with the large number of existing prediction servers and the constant changes in the prediction methods.  ...  We are grateful to members of the Protein Design Group. The contribution of the PDG is supported in part by a grant from the Spanish Ministry of Science and Technology (PDG, CNB-CSIC).  ... 
doi:10.1093/nar/gkg619 pmid:12824315 pmcid:PMC169025 fatcat:pw6i345cfzbfxemqsuc5ytglmq

CAFASP3 in the spotlight of EVA

Volker A. Eyrich, Dariusz Przybylski, Ingrid Y.Y. Koh, Osvaldo Grana, Florencio Pazos, Alfonso Valencia, Burkhard Rost
2003 Proteins: Structure, Function, and Bioinformatics  
This assessment was carried out in the framework of the fully automated, web-based evaluation server EVA. Detailed results are available at http://cubic.bioc.columbia.edu/eva/ cafasp3/.  ...  We have analysed fold recognition, secondary structure and contact prediction servers from CAFASP3.  ...  IK was supported by the grant 5-P20-LM7276 from the National Institute of Health (NIH), DP and BR were supported by the NIH grant RO1-GM63029-01.  ... 
doi:10.1002/prot.10534 pmid:14579345 fatcat:e7zh5hfbuvcd5eaes2yiwhcsg4

EVA: Large-scale analysis of secondary structure prediction

Burkhard Rost, Volker A. Eyrich
2001 Proteins: Structure, Function, and Bioinformatics  
EVA is a web-based server that evaluates automatic structure prediction servers continuously and objectively. Since June 2000, EVA collected more than 20,000 secondary structure predictions.  ...  The EVA sets sufficed to conclude that the field of secondary structure prediction has advanced again.  ...  ACKNOWLEDGMENTS We thank the EVA teams at the Rockefeller University (Marc A.  ... 
doi:10.1002/prot.10051 pmid:11835497 fatcat:oyymkg5dd5dd7ouzfdxuvc7chu

BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra

András Micsonai, Frank Wien, Éva Bulyáki, Judit Kun, Éva Moussong, Young-Ho Lee, Yuji Goto, Matthieu Réfrégiers, József Kardos
2018 Nucleic Acids Research  
Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification.  ...  The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data.  ...  The second module, the 'Fold recognition' module of the server is used to predict the fold of a protein from secondary structure contents provided by the user.  ... 
doi:10.1093/nar/gky497 pmid:29893907 pmcid:PMC6031044 fatcat:bqxaio6cr5b57mx6a7zs7vegbi

EVAcon: a protein contact prediction evaluation service

O. Grana, V. A. Eyrich, F. Pazos, B. Rost, A. Valencia
2005 Nucleic Acids Research  
EVAcon is a new service added to the functionality of the EVA system for the continuous evaluation of protein structure prediction servers.  ...  Currently, EVAcon is monitoring nine servers, four of which are specialized in contact prediction and five are general structure prediction servers.  ...  We also thank the protein structure prediction community for making their methods available as public webservers, and in particular to those that allow us to assess their results in the context of EVA.  ... 
doi:10.1093/nar/gki411 pmid:15980486 pmcid:PMC1160172 fatcat:7ffnqv4izbdthdax6me66eq7oy

ProteinsPlus: interactive analysis of protein-ligand binding interfaces

Katrin Schöning-Stierand, Konrad Diedrich, Rainer Fährrolfes, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Ruben Steinegger, Matthias Rarey
2020 Nucleic Acids Research  
water molecules in the ligand binding sites of a protein, and METALizer calculates, predicts and scores coordination geometries of metal ions based on surrounding complex atoms.  ...  Due to the increasing amount of publicly available protein structures searching, enriching and investigating these data still poses a challenging task.  ...  The analysis performed by Structure-Profiler can be divided into four different areas: First, the quality of the experimental data is evaluated using the resolution of the protein structure, its diffraction  ... 
doi:10.1093/nar/gkaa235 pmid:32297936 pmcid:PMC7319454 fatcat:kd6f4rcq65cc7fbz2dgllf5rva

Community-based gene structure annotation

Shannon D. Schlueter, Matthew D. Wilkerson, Eva Huala, Seung Y. Rhee, Volker Brendel
2005 Trends in Plant Science  
We thank Michael Lawler and Stephanie Haila, both school science teachers in Iowa, for working with us to develop the gene structure annotation tutorial.  ...  Quality assessment of predicted gene structures Alignments are first evaluated to determine their native locus and, if necessary, the specific transcript isoform derived from the locus.  ...  (b) Evidence of the false prediction of an intergenic region, necessitating the union of two adjacent gene structure predictions. 76 other such cases can be found.  ... 
doi:10.1016/j.tplants.2004.11.002 pmid:15642518 fatcat:btg5anweavd4lbeewdyo72txey

The Assessment of Methods for Protein Structure Prediction [chapter]

Anna Tramontano, Domenico Cozzetto, Alejandro Giorgetti, Domenico Raimondo
2008 Protein Structure Prediction  
These are the questions that this chapter tries to address, by describing automatic evaluation methods as well as the world-wide Critical Assessment of Techniques for Protein Structure Prediction (CASP  ...  Methods for protein structure prediction are flourishing and becoming widely available to both experimentalists and computational biologists. But, how good are they?  ...  This need has prompted the development of automatic systems that continuously evaluate automatic prediction methods.  ... 
doi:10.1007/978-1-59745-574-9_2 pmid:18075161 fatcat:242sjgq5rbg7lafmepq54qslri

BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy

András Micsonai, Éva Moussong, Frank Wien, Eszter Boros, Henrietta Vadászi, Nikoletta Murvai, Young-Ho Lee, Tamás Molnár, Matthieu Réfrégiers, Yuji Goto, Ágnes Tantos, József Kardos
2022 Nucleic Acids Research  
It overperforms any available method in accuracy and information content, moreover, it is capable of predicting the protein fold down to the topology/homology level of the CATH classification.  ...  β-structured proteins.  ...  The advantage of using CATH is that most of the protein domains in the PDB are classified and the database is continuously maintained.  ... 
doi:10.1093/nar/gkac345 pmid:35544232 fatcat:qut7zl3nkjdzzclrvpsjug23ya

Critical assessment of methods of protein structure prediction (CASP)-round V

John Moult, Krzysztof Fidelis, Adam Zemla, Tim Hubbard
2003 Proteins: Structure, Function, and Bioinformatics  
This article provides an introduction to the special issue of the journal Proteins dedicated to the fifth CASP experiment to assess the state of the art in protein structure prediction.  ...  The article describes the conduct, the categories of prediction, and the evaluation and assessment procedures of the experiment.  ...  The nature of the prediction field continues to change rapidly, with additional sources of prediction targets, increasing importance of automatic prediction servers, and a growing role of benchmarking  ... 
doi:10.1002/prot.10556 pmid:14579322 fatcat:c7nkq3nwd5ggzhhmnabgxx5ryi

Servers for protein structure prediction

Daniel Fischer
2006 Current Opinion in Structural Biology  
Recent experiments suggest that servers will soon free humans from most of the burden of protein structure prediction.  ...  As a result of structural genomics and genome sequencing projects, and significant improvements in the performance of protein structure prediction methods, a generation of automated servers has evolved  ...  LB continuously assesses the capabilities of automated servers using a relatively large number of prediction targets, compiled every week from newly released protein structures, and provides an evaluation  ... 
doi:10.1016/j.sbi.2006.03.004 pmid:16546376 fatcat:5jceg2fdg5c5joneabirotj7mi

BeStSel: From Secondary Structure Analysis to Protein Fold Prediction by Circular Dichroism Spectroscopy [chapter]

András Micsonai, Éva Bulyáki, József Kardos
2020 Msphere  
Moreover, BeStSel provides extra information on the orientation and twist of the β-sheets which is sufficient for the prediction of the protein fold.  ...  of proteins containing this secondary structure component.  ...  This module of the BeStSel server is useful to compare the secondary structure results to the available reference protein structures.  ... 
doi:10.1007/978-1-0716-0892-0_11 pmid:33125651 fatcat:4f5tweywpffzdhh2xssd56xjdq

META-PP: single interface to crucial prediction servers

V. A. Eyrich
2003 Nucleic Acids Research  
The META-PP server (http://cubic.bioc.columbia. edu/meta/) simplifies access to a battery of public protein structure and function prediction servers by providing a common and stable web-based interface  ...  At present META-PP provides access to a selected set of high-quality servers in the areas of comparative modelling, threading/fold recognition, secondary structure prediction and more specialized fields  ...  The work of B.R. was supported by grants 1-P50-GM62413-01 and RO1-GM63029-01 from the National Institute of Health (NIH), and the grant DBI-0131168 from the National Science Foundation (NSF).  ... 
doi:10.1093/nar/gkg572 pmid:12824314 pmcid:PMC168978 fatcat:v7su4cpb5ncvrn7hmfkde6tfri

GeneSilico protein structure prediction meta-server

M. A. Kurowski
2003 Nucleic Acids Research  
We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input.  ...  The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta.  ...  ACKNOWLEDGEMENTS We are grateful to developers of the protein fold recognition servers who kindly agreed to have them included in our metaserver, in particular Drs Arne Elofsson, Daniel  ... 
doi:10.1093/nar/gkg557 pmid:12824313 pmcid:PMC168964 fatcat:fryudy4xejaslg3mja7s37lxku
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