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Accurate Quantification of Functional Analogy among Close Homologs

Maria D. Chikina, Olga G. Troyanskaya, Richard Bonneau
2011 PLoS Computational Biology  
We demonstrate that even among closely related genes, our method is able to predict functionally analogous homolog pairs better than relying on sequence comparison alone.  ...  Correctly evaluating functional similarities among homologous proteins is necessary for accurate transfer of experimental knowledge from one organism to another, and is of particular importance for the  ...  that functional predictions which are accurate on average over all genes will be accurate on average over families of close homologs.  ... 
doi:10.1371/journal.pcbi.1001074 pmid:21304936 pmcid:PMC3033368 fatcat:llosbs62vrgwncx4mtqcvh5zf4

Quantifying Homologous Proteins and Proteoforms

Dmitry Malioutov, Tianchi Chen, Edoardo Airoldi, Jacob Jaffe, Bogdan Budnik, Nikolai Slavov
2018 Molecular & Cellular Proteomics  
However, their quantification by existing bottom-up mass-spectrometry (MS) methods is undermined by peptide-specific biases.  ...  Many proteoforms - arising from alternative splicing, post-translational modifications (PTMs), or paralogous genes - have distinct biological functions, such as histone PTM proteoforms.  ...  HIquant's utility is particularly relevant when proteins and proteoforms have comparable abundances (within 10-100 fold difference) but distinct functions (Slavov et al., 2015) and thus accurate quantification  ... 
doi:10.1074/mcp.tir118.000947 pmid:30282776 fatcat:3mse7rn42nbrzi7u4sk7bypfju

Quantifying homologous proteins and proteoforms [article]

Dmitry Malioutov, Tianchi Chen, Jacob Jaffe, Edoardo Airoldi, Steven Carr, Bogdan Budnik, Nikolai Slavov
2017 bioRxiv   pre-print
However, their quantification by existing bottom-up mass-spectrometry (MS) methods is undermined by peptide-specific biases.  ...  Many proteoforms - arising from alternative splicing, post-translational modifications (PTMs), or paralogous genes - have distinct biological functions, such as histone PTM proteoforms.  ...  HIquant's utility is particularly relevant when proteins and proteoforms have comparable abundances (within 10-100 fold difference) but distinct functions (Slavov et al., 2015) and thus accurate quantification  ... 
doi:10.1101/168765 fatcat:oyjer2kr5ffbnd7eojvwvw3hmm

Three-dimensional geometric morphometrics for studying floral shape variation

Timotheüs van der Niet, Christoph P.E. Zollikofer, Marcia S. Ponce de León, Steven D. Johnson, H. Peter Linder
2010 Trends in Plant Science  
), which are considered some of the most structurally complex among the angiosperms.  ...  We found that the resulting 3D geometric representation of the flowers matched real flowers very closely (Figure 1 ).  ...  The editor and three anonymous reviewers are kindly acknowledged for providing useful comments on an earlier version of the manuscript.  ... 
doi:10.1016/j.tplants.2010.05.005 pmid:20541450 fatcat:cgl2ewfhjjfaxan5dwmxbbcb5e

Olfactory psychometric functions for homologous 2-ketones

J. Enrique Cometto-Muñiz, Michael H. Abraham
2009 Behavioural Brain Research  
., psychometric) odor functions for the homologous ketones propanone (acetone), 2-pentanone, 2-heptanone, and 2-nonanone.  ...  ., psychometric) odor functions for the homologous ketones propanone (acetone), 2-pentanone, 2-heptanone, and 2-nonanone.  ...  In turn, Table 3 provides a quantification of each individual function in terms of the constants C and D, and of R 2 .  ... 
doi:10.1016/j.bbr.2009.02.014 pmid:19428635 pmcid:PMC2709282 fatcat:upll3wbbzvb5hp3elhdp7qzeka

Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics

Artem Cherkasov, Shannan J Ho Sui, Robert C Brunham, Steven J M Jones
2004 BMC Bioinformatics  
We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function.  ...  We have found that the Weibull function describes protein fold distribution within and among genomes more accurately than conventional power functions which have been used in a number of structural genomic  ...  Boris Sobolev (Clinical Epidemiology and Statistics, UBC) for valuable inputs and help with statistical analysis of genomic data with the SAS.  ... 
doi:10.1186/1471-2105-5-101 pmid:15274750 pmcid:PMC499543 fatcat:hsyfk6siqbbjdbcb3cr66i5pc4

Guanidinium Toxins and Their Interactions with Voltage-Gated Sodium Ion Channels

Lorena Durán-Riveroll, Allan Cembella
2017 Marine Drugs  
The functional role in aquatic and terrestrial ecosystems for both groups of toxins is unproven, although plausible mechanisms of ion channel regulation and chemical defense are often invoked.  ...  In contrast, toxins of the TTX group occur mainly in macrozoa, particularly among puffer fish, several species of marine invertebrates and a few terrestrial amphibians.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/md15100303 pmid:29027912 pmcid:PMC5666411 fatcat:me7fwga6nfarzbqkwmmp2ux57y

The conserved arginine 380 of Hsp90 is not a catalytic residue, but stabilizes the closed conformation required for ATP hydrolysis

Christian N. Cunningham, Daniel R. Southworth, Kristin A. Krukenberg, David A. Agard
2012 Protein Science  
of structural and functional approaches.  ...  While the R380A mutation compromised ATPase activity in all three homologs, the impact on ATPase activity was both variable and much more modest (2-7 fold) than the mutation of an active site glutamate  ...  Acknowledgments The authors thank the entirety of the Agard Lab for many helpful discussions and comments.  ... 
doi:10.1002/pro.2103 pmid:22653663 pmcid:PMC3537237 fatcat:twpnhwvdlve7pfso2gskkljq6q

Quantification of Chemical Vapors in Chemosensory Research

J. E. Cometto-Muniz
2003 Chemical Senses  
For more than a decade now, our systematic studies of the olfactory and chemesthetic potency of members of homologous chemical series have routinely included quantification of vapors via gas chromatography  ...  The paper represents a step toward creation of a practical archive for vapor quantification in chemosensory science.  ...  Preparation of this article was supported by research grant number R01 DC02741 from the National Institute on Deafness and Other Communication Disorders, National Institutes of Health.  ... 
doi:10.1093/chemse/28.6.467 pmid:12907584 fatcat:syoy2dsgpbaebmwqjxez5rguzy

Medicago truncatula DMI1 Required for Bacterial and Fungal Symbioses in Legumes

J.-M. Ane
2004 Science  
The biological and molecular function of this group of proteins is likely to be conserved because of the high degree of conservation for DMI1 orthologs among angiosperms (Ͼ80% similarity among rice, Arabidopsis  ...  are present in the N-terminus of DMI1, a region of the protein that is poorly conserved among the various homologs.  ...  The screen described here provides a comprehensive analysis of the genes required for the meiotic cell cycle and identifies three factors important for the stepwise loss of sister chromatid cohesion.  ... 
doi:10.1126/science.1092986 pmid:14963334 fatcat:6cm6hwpfwvabbknkxq5sbgpofm

ON THE PROBLEM OF IDENTIFYING HOMOLOGIES IN LITHIC ARTIFACTS [chapter]

Gustavo Barrientos
2016 Darwin´s Legacy: The Status of Evolutionary Archaeology in Argentina  
ACKNOWLEDGEMENTS To the convenors of the meeting "Arqueología Argentina y el Legado de Charles Darwin" (Argentine Archaeology and the Legacy of  ...  parts in every variety of form and function, and analogy, i.e. similarity of parts in their functional adaptations.  ...  These and closely related issues, like the assessing and quantification of the relative contribution of informational and environmental factors to the constitution of artifactual phenotypes, should integrate  ... 
doi:10.2307/j.ctv1zcm1c0.8 fatcat:2l4rqo5mjbb2hgi4llp32qre5m

Potential for Development of an Escherichia coli—Based Biosensor for Assessing Bioavailable Methionine: A Review

Vesela I. Chalova, Clifford Froelich, Steven C. Ricke
2010 Sensors  
E. coli as a Biosensor Among all microorganisms, E. coli is one of the most highly investigated bacteria for the purposes of biosensor fabrication.  ...  Methionine deficiency or excess in animal diets can lead to sub-optimal animal performance and increased environmental pollution, which necessitates its accurate quantification and proper dosage in animal  ...  could be accurately used in the quantification of methionine, tryptophan, and lysine bioavailability.  ... 
doi:10.3390/s100403562 pmid:22319312 pmcid:PMC3274233 fatcat:rg2e37ae4rcc7nrcgndz7dllqq

Comparing Dirichlet normal surface energy of tooth crowns, a new technique of molar shape quantification for dietary inference, with previous methods in isolation and in combination

Jonathan M. Bunn, Doug M. Boyer, Yaron Lipman, Elizabeth M. St. Clair, Jukka Jernvall, Ingrid Daubechies
2011 American Journal of Physical Anthropology  
Inferred dietary preference is a major component of paleoecologies of extinct primates.  ...  Five shape quantification metrics were calculated on each molar: DNE, shearing quotient, shearing ratio, relief index, and orientation patch count rotated (OPCR). in Wiley Online Library (wileyonlinelibrary.com  ...  Judex for access to micro-CT scanning facilities in Center for Biotechnology of SBU. LITERATURE CITED  ... 
doi:10.1002/ajpa.21489 pmid:21469070 fatcat:cma3n4a2rjdzxkv3eoya4tcbsa

Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles

Paul Wilmes, Philip L Bond
2009 Current Opinion in Microbiology  
Major limitations associated with the 2DE approach are comigration of proteins into discrete spots hampering accurate quantification and identification [9] .  ...  of community structure and function.  ...  References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as: of special interest of outstanding interest  ... 
doi:10.1016/j.mib.2009.03.004 pmid:19414280 fatcat:ffcx66gbmjgzlnhaqoaidkg5b4

Multiple Sequence Alignment is not a Solved Problem [article]

David A. Morrison
2018 arXiv   pre-print
Consequently, almost all algorithms developed for multiple sequence alignment are based on optimizing some sort of compositional similarity (similarity = homology + analogy).  ...  What is needed is a program that evaluates all of the evidence for the sequence homologies, optimizes their combination, and thus produces the best hypotheses of homology.  ...  homology = similarity of structure, whereas analogy = similarity of function).  ... 
arXiv:1808.07717v1 fatcat:du2jcnjyozcojmh6zwqnkdo7yy
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