Filters








120,658 Hits in 8.1 sec

Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments

A. W. Slater, J. I. Castellanos, M. J. Sippl, F. Melo
2012 Bioinformatics  
Results: Here we report on the development and application of a new approach for the evaluation of structure alignment results.  ...  Hence, at the current state of development of structure comparison techniques, it is advisable to use several programs in parallel and to choose the optimal alignment in the way reported here.  ...  Similar strategies may eventually be developed in the future for alternative measures, thus allowing the comparison of software performance from distinct point of views.  ... 
doi:10.1093/bioinformatics/bts600 pmid:23060612 fatcat:b744ktpvtnfvjjxn7oibz2vd6e

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

Tomasz Puton, Lukasz P. Kozlowski, Kristian M. Rother, Janusz M. Bujnicki
2013 Nucleic Acids Research  
As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank.  ...  We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server.  ...  ACKNOWLEDGEMENTS The authors thank the developers of RNA structure prediction methods analyzed in this work for making them freely available.  ... 
doi:10.1093/nar/gkt101 pmid:23435231 pmcid:PMC3627593 fatcat:46y43oiui5bb3kobe6rakzgqgq

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  
Both evaluations ranked a semiautomated method named CAFASP-CONSENSUS, that filed predictions using the CAFASP results of the servers, above any of the individual servers.  ...  The CAFASP evaluation indicated that it is difficult to establish an exact ranking of the servers because the number of prediction targets was relatively small and the differences among many servers were  ...  Evaluation method Model evaluation was based on a new method for structural alignment and comparison, which enables us to compare an experimental protein structure with an arbitrary low-resolution three-dimensional  ... 
doi:10.1002/prot.10036 pmid:11835495 fatcat:llmxmpcec5f7vfwatkyyqb2chi

MaxSub: an automated measure for the assessment of protein structure prediction quality

N. Siew, A. Elofsson, L. Rychlewski, D. Fischer
2000 Bioinformatics  
Motivation: Evaluating the accuracy of predicted models is critical for assessing structure prediction methods.  ...  Results: MaxSub is a new and independently developed method that further builds and extends some of the evaluation methods introduced at CASP3.  ...  We acknowledge Adam Zemla for developing GDT. We thank Manfred Sippl for critically reading the manuscript and  ... 
doi:10.1093/bioinformatics/16.9.776 pmid:11108700 fatcat:aokvfyn3nzfszgfwvntjzbbnza

EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments

Jean-Christophe Gelly, Laurent Chiche, Jérôme Gracy
2005 BMC Bioinformatics  
We propose a fully automatic method for the classification of structural environments and inference of structure-dependent substitution profiles.  ...  The resulting structure-dependent substitution scores were assessed using a criterion based on the mean ranking of observed substitution among all possible substitutions and in sequence-structure alignments  ...  Moreover, comparison of the EvDTree substitution scores with other scoring functions for sequence-structure alignments led to results similar to the mean rank evaluation supporting the usefulness of the  ... 
doi:10.1186/1471-2105-6-4 pmid:15638949 pmcid:PMC545998 fatcat:aeihrebp3jehhnn2jnf6uhcndu

Hybrid Fold Recognition: Combining Sequence Derived Properties with Evolutionary Information

Daniel Fischer
1999 Biocomputing 2000  
Recent assessments of structure prediction have demonstrated that i although fold recognition methods can often identify remote similarities when standard sequence search methods fail, the score of the  ...  over a wide range of targets, and v extensive h uman-expert intervention is usually required for the most di cult prediction targets.  ...  Acknowledgments: Thanks to Erez Karpas for his assistance in setting up the bioinbgu server and to the anonymous referees for their helpful comments.  ... 
doi:10.1142/9789814447331_0012 fatcat:3o46rs6bk5gqzpjqjc2xicqh7y

The iRMSD: a local measure of sequence alignment accuracy using structural information

F. Armougom, S. Moretti, V. Keduas, C. Notredame
2006 Bioinformatics  
Motivation: We introduce the iRMSD, a new type of RMSD, independent from any structure superposition and suitable for evaluating sequence alignments of proteins with known structures.  ...  Results: We demonstrate that the iRMSD is equivalent to the standard RMSD although much simpler to compute and we also show that it is suitable for comparing sequence alignments and benchmarking multiple  ...  Jean-Michel Claverie (head of IGS) for useful discussions and material support. We also thank Dr Phillip Bucher who provided many of the original ideas through useful discussions.  ... 
doi:10.1093/bioinformatics/btl218 pmid:16873492 fatcat:6zervrknjbdppphudrg477o62y

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools

2019 Nucleic Acids Research  
The RNA-Puzzles contest has shown, among others, that the development and validation of computational methods for RNA fold prediction strongly depend on the benchmark datasets and the structure comparison  ...  Here, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods (raw, for-evaluation and standardized datasets), (ii)  ...  The structure data from this resource is a good starting point for developing and benchmarking model ranking methods (20) .  ... 
doi:10.1093/nar/gkz1108 pmid:31799609 pmcid:PMC7145511 fatcat:aua3ozugyzdzxoylcobu6fle7u

Strategic Alignment of ICT Projects with Community Values in Local Government

Marcus Vogt, Kieth Hales
2010 2010 43rd Hawaii International Conference on System Sciences  
Achieving strategic alignment is a major governance concern in both the private and public sectors, but many of the private sector's, financially focused evaluation methodologies are less useful in the  ...  A new methodology: Community Value Estimation (CVE), which combines the Analytic Hierarchy Process (AHP) and the Delphi technique, is introduced and demonstrated as an important method of combining public  ...  Figure 2 . 2 BVIT Project Priorities Figure 7 7 shows the CVE ranking of 20 projects. For comparison the original BVIT ranking of the projects are shown in parenthesis. Archer, N.  ... 
doi:10.1109/hicss.2010.350 dblp:conf/hicss/VogtH10 fatcat:jqx2ait4mfeivaj7vskbssvkni

LiveBench-2: Large-scale automated evaluation of protein structure prediction servers

Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski
2001 Proteins: Structure, Function, and Bioinformatics  
and in order to help the developers to analyze and improve the services.  ...  The aim of the LiveBench experiment is to provide a continuous evaluation of structure prediction servers in order to inform potential users about the current state-of-the-art structure prediction tools  ...  Second, this evaluation method ignores the accuracy of the alignment, which is often crucial for the confirmation of the predicted function (for example through comparison of aligned active site residues  ... 
doi:10.1002/prot.10039 pmid:11835496 fatcat:crdzr3sglrf4xhtm3uhtk7bxl4

LiveBench-6: Large-scale automated evaluation of protein structure prediction servers

Leszek Rychlewski, Daniel Fischer, Arne Elofsson
2003 Proteins: Structure, Function, and Bioinformatics  
and in order to help the developers to analyze and improve the services.  ...  The aim of the LiveBench experiment is to provide a continuous evaluation of structure prediction servers in order to inform potential users about the current state-of-the-art structure prediction tools  ...  Second, this evaluation method ignores the accuracy of the alignment, which is often crucial for the confirmation of the predicted function (for example through comparison of aligned active site residues  ... 
doi:10.1002/prot.10535 pmid:14579344 fatcat:bddsds5f3nf3hj43uao5vwphwu

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  
We compared methods from all categories to experts in secondary structure and contact prediction and homology modellers to fold recognisers.  ...  We observed that the sequence-unique targets from CAFASP3/CASP5 were not fully representative for evaluating performance. For all three categories, we showed how careless ranking might be misleading.  ...  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

MUFOLD: A new solution for protein 3D structure prediction

Jingfen Zhang, Qingguo Wang, Bogdan Barz, Zhiquan He, Ioan Kosztin, Yi Shang, Dong Xu
2009 Proteins: Structure, Function, and Bioinformatics  
Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD.  ...  The average root-mean-square deviation of the best models from the native structures is 4.28 Å, which shows significant and systematic improvement over our previous methods.  ...  Acknowledgments Major computer time was provided by the University of Missouri Bioinformatics Consortium. The authors thank Jianlin Cheng, Yang Zhang, and Joel L. Sussman for helpful discussions.  ... 
doi:10.1002/prot.22634 pmid:19927325 pmcid:PMC2885889 fatcat:x6udc5gwbbg5tokkdwzu5vuxh4

ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information

Daniel Barthel, Jonathan D Hirst, Jacek Błażewicz, Edmund K Burke, Natalio Krasnogor
2007 BMC Bioinformatics  
It employs the Universal Similarity Metric (USM), the Maximum Contact Map Overlap (MaxCMO) of protein structures and other external methods such as the DaliLite and the TM-align methods, the Combinatorial  ...  We introduce the decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information (ProCKSI ).  ...  Recently, they have also been used for the evaluation of structural similarity and alignment methods [88, 92, 93] .  ... 
doi:10.1186/1471-2105-8-416 pmid:17963510 pmcid:PMC2222653 fatcat:oyp7ubgfdff3xaoi4gjmvjtj5m

CSmetaPred: a consensus method for prediction of catalytic residues

Preeti Choudhary, Shailesh Kumar, Anand Kumar Bachhawat, Shashi Bhushan Pandit
2017 BMC Bioinformatics  
The visual and quantitative analysis of ROC and PR curves shows that meta-predictors outperform their constituent methods and CSmetaPred_poc is the best of evaluated methods.  ...  Despite significant development in active-site prediction methods, one of the remaining issues is ranked positions of putative catalytic residues among all ranked residues.  ...  Acknowledgments Swapnil Tichkule helped in manually identifying enzymes from PDB database for predictions discussed in case studies section of the manuscript.  ... 
doi:10.1186/s12859-017-1987-z pmid:29273005 pmcid:PMC5741869 fatcat:dwwmuo6nwzao5ndis6aql6ib7i
« Previous Showing results 1 — 15 out of 120,658 results