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Unique identifier OMICS_15815
Name LiveBench
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained No

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Publications for LiveBench

LiveBench citations

 (16)
library_books

General overview on structure prediction of twilight zone proteins

2015
PMCID: 4559291
PMID: 26338054
DOI: 10.1186/s12976-015-0014-1

[…] ell as the physiochemical properties of amino acids [–] to improve the quality of the built model. The scoring function e.g. position specific scoring matrices (PSSMs), Levitt-Gerstein (LG) score [], LiveBench [], MaxSub [], S-score [], C-score [] where then used to rank the built models. Besides, obtaining an accurate structure for twilight-zone protein is challenging []. For this reason, this re […]

library_books

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

2013
Nucleic Acids Res
PMCID: 3627593
PMID: 23435231
DOI: 10.1093/nar/gkt101

[…] ys of calculating the rankings, in which any of the methods tested could score better. The same problem concerns methods for protein structure prediction, yet rigorous benchmarks, in particular CASP, Livebench and EVA, have greatly contributed to the progress in the field of protein structure prediction [review: ()]. Recently, a CASP-like benchmark called RNA Puzzles has been organized: it involve […]

library_books

BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles

2012
Nucleic Acids Res
PMCID: 3394251
PMID: 22693216
DOI: 10.1093/nar/gks555

[…] e to profile aligning methods are among the best-performing present-day methods for fold recognition, as can be seen from the results of the blind, automated structure prediction contests CASP () and LIVEBENCH (,).In this contribution, we present a new fully automated 1D threading server. Its unique element is the combination of three different secondary structure prediction methods in the scoring […]

library_books

RNA and protein 3D structure modeling: similarities and differences

2011
J Mol Model
PMCID: 3168752
PMID: 21258831
DOI: 10.1007/s00894-010-0951-x

[…] ingful analysis is probably still too small to provide a sufficient number of targets for CASP-like intense modeling over a few months every year. In the meantime we have started a project similar to Livebench (again, an inspiration from the field of protein structural bioinformatics), which aims to become an objective benchmark of fully automated methods for RNA structure prediction. The CompaRNA […]

library_books

TIM Finder: A new method for identifying TIM barrel proteins

2009
BMC Struct Biol
PMCID: 2803183
PMID: 20003393
DOI: 10.1186/1472-6807-9-73

[…] types of structural and sequence information, have been widely demonstrated in a series of CASP experiments [], as well as in some real-time evaluation systems of structure prediction servers (e.g., LiveBench) [].The advantage of the above methods is that they are suitable for many protein fold types, but they may lack the specificity to recognize certain folds. Therefore, it is necessary to deve […]

library_books

Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human

2009
Nucleic Acids Res
PMCID: 2794190
PMID: 19833706
DOI: 10.1093/nar/gkp854

[…] reover, the high divergence of some NTase fold families that is likely reflected as lower than threshold (<40) Meta-BASIC scores was also considered. According to rigorous structural criteria used in LiveBench benchmarks (http://meta.bioinfo.pl/results.pl?comp_name=livebench-2008.2), predictions with scores above 40 have less than 5% probability of being incorrect. Specifically, in addition to hig […]

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