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Rate4Site specifications

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Unique identifier OMICS_06940
Name Rate4Site
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Itay Mayrose

Publication for Rate4Site

Rate4Site citations

 (64)
library_books

Measuring evolutionary rates of proteins in a structural context

2018
F1000Res
PMCID: 5676193
PMID: 29167739
DOI: 10.5256/f1000research.13954.r27048

[…] calculate evolutionary rates, hyphy’s fel and leisr approaches. as an alternative method to measuring amino acid evolutionary rates with leisr, we presented a brief pipeline in the notes that uses rate4site software. other methods for calculating evolutionary rates have been provided by rodrigue et al. and tamuri et al. – , whose methods infer codon-level site-wise evolutionary rates […]

library_books

Comparative phosphoproteomic analysis reveals signaling networks regulating monopolar and bipolar cytokinesis

2018
Sci Rep
PMCID: 5797227
PMID: 29396449
DOI: 10.1038/s41598-018-20231-5

[…] extent monopolar and bipolar cytokinesis specific phosphosites are evolutionary conserved. the conservation scores of each site, on a scale from 9 (the most conserved) to 1, were calculated using rate4site. strikingly, those phosphopeptides that are common to both monopolar and bipolar cytokinesis are the most conserved ones. the distribution of the phosphopeptides in this category is skewed […]

library_books

A novel Gerstmann Sträussler Scheinker disease mutation defines a precursor for amyloidogenic 8 kDa PrP fragments and reveals N terminal structural changes shared by other GSS alleles

2018
PLoS Pathog
PMCID: 5786331
PMID: 29338055
DOI: 10.1371/journal.ppat.1006826

[…] scored and clustered resulting in 10 models for each of three scoring methods (interevscore, soap_pp atom-based statistical potential, and frodock). conservation of residues was assessed with the rate4site., procedures for the index case have already been described []. all other procedures were performed under protocols approved by the institutional review board at case western reserve […]

library_books

Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum

2018
Biotechnol Biofuels
PMCID: 5766984
PMID: 29344086
DOI: 10.1186/s13068-017-1006-7

[…] was selected. the gh7 cbh catalytic domains were realigned by clustalw using mega7 software [], followed by indel elimination. this alignment was analyzed by rca as described earlier []. in short, rate4site (version 2.01) was used to calculate the degree of conservation (s score) for each amino acid position using the empirical bayesian method [, ]. a sliding window-average (n = 7) s score […]

library_books

Relative evolutionary rate inference in HyPhy with LEISR

2018
PeerJ
PMCID: 5804317
PMID: 29423346
DOI: 10.7717/peerj.4339

[…] (likehood estimation of individual site rates, pronounced “laser”), a tool to infer relative evolutionary rates from protein and nucleotide data, implemented in hyphy. leisr is based on the popular rate4site () approach for inferring relative site-wise evolutionary rates, primarily from protein data. we extend the original method for more general use in several key ways: (i) we increase […]

library_books

Protein protein binding selectivity and network topology constrain global and local properties of interface binding networks

2017
Sci Rep
PMCID: 5514078
PMID: 28717235
DOI: 10.1038/s41598-017-05686-2

[…] in the 56 yeast cme proteins and 127 human erbb proteins, we collected orthologs of each protein, ran multiple sequence alignments with mafft, and analyzed residue conservation with the consurf rate4site program (or web-server). to assign a conservation score to each domain, the average over all residues in the domain were taken (table ). orthologs were constructed from blast searches […]


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Rate4Site institution(s)
Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel

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