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RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins

Rasna R. Walia, Li C. Xue, Katherine Wilkins, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar, Lukasz Kurgan
2014 PLoS ONE  
Sequence-based computational methods offer a viable, cost-effective way to identify putative RNA-binding residues in RNA-binding proteins.  ...  RNABindRPlus was able to predict RNA-binding residues of all proteins in both test sets, achieving an MCC of 0.55 and 0.37, respectively, and outperforming all other methods, including those that make  ...  Acknowledgments We thank members of the Dobbs and Honavar groups for useful discussions and Carla Mann for assistance in generating the RB111 dataset. The authors sincerely thank Janusz M.  ... 
doi:10.1371/journal.pone.0097725 pmid:24846307 pmcid:PMC4028231 fatcat:nbmt6fzzvngu3hvltbgoecnozq

Searching sequence space for protein catalysts

S. V. Taylor, K. U. Walter, P. Kast, D. Hilvert
2001 Proceedings of the National Academy of Sciences of the United States of America  
Genetic selection was used to explore the probability of finding enzymes in protein sequence space.  ...  and four nonpolar residues.  ...  The publication costs of this article were defrayed in part by page charge payment.  ... 
doi:10.1073/pnas.191159298 pmid:11535813 pmcid:PMC58511 fatcat:bwglgv46qveohfkqp445r6a4yy

Sequence and structure space of RNA-binding peptides

Chandreyee Das, Alan D. Frankel
2003 Biopolymers  
Studies of RNA-binding peptides, and recent combinatorial library experiments in particular, have demonstrated that diverse peptide sequences and structures can be used to recognize specific RNA sites.  ...  The high frequency at which RNA-binding peptides are found in large sequence libraries suggests plausible routes to evolve sequence-specific binders, facilitating the design of new binding molecules and  ...  in the ␣-helix conserving the Zif268 sequence, and four of the remaining five residues being positively charged, suggesting that electrostatic interactions were highly enriched in this selection experiment  ... 
doi:10.1002/bip.10429 pmid:12925994 fatcat:jkavgrjdr5bn3cljqggixpy52y

Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets

Yi-Yuan Chiu, Chun-Yu Lin, Chih-Ta Lin, Kai-Cheng Hsu, Li-Zen Chang, Jinn-Moon Yang
2012 BMC Genomics  
Among 356 pharma-motifs, 56.5% interacting residues are highly conserved.  ...  In general, the polypharmacological proteins often share similar local binding environments and motifs.  ...  Acknowledgements This paper was supported by National Science Council, partial supports of Ministry of Education and National Health Research Institutes (NHRI-EX100-10009PI).  ... 
doi:10.1186/1471-2164-13-s7-s21 pmid:23281852 pmcid:PMC3521469 fatcat:vk2ot5w2yrh57nhccuvcnp62pe

Cooperative "folding transition" in the sequence space facilitates function-driven evolution of protein families

Akira R. Kinjo
2018 Journal of Theoretical Biology  
Furthermore, enforcing or suppressing consensus residues on a few of the well-conserved sites enhanced or diminished, respectively, the natural-like pattern formation over the entire sequence.  ...  In most families, the key sites included ligand binding sites.  ...  Acknowledgements The author thanks Ken Nishikawa, Motonori Ota and Gautam Basu for valuable comments, Eugene I. Shakhnovich for providing some references.  ... 
doi:10.1016/j.jtbi.2018.01.019 pmid:29355538 fatcat:e5cpvwfvbbgnva3dd43hldltyi

The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing

A. J. Dombroski, B. D. Johnson, M. Lonetto, C. A. Gross
1996 Proceedings of the National Academy of Sciences of the United States of America  
spacing of 17 bp. a, factors have two distinct DNA binding domains that recognize the two hexamer sequences.  ...  Furthermore, a mutant cr, selected for increasing transcription of the minimal lac promoter (18-bp spacer), has an altered response to promoter spacing in vivo and in vitro.  ...  ., and American Cancer Society Grant PF-3408 and Grant 94G-263 from the Texas Affiliate of the American Heart Association to A.J.D.  ... 
doi:10.1073/pnas.93.17.8858 pmid:8799117 pmcid:PMC38558 fatcat:vx53lpigkvbgfczlkastlio5su

Visualizing the dual space of biological molecules

John Eargle, Zaida Luthey-Schulten
2006 Computational biology and chemistry  
An important part of protein structure characterization is the determiniation of excluded space such as fissures in contact interfaces, pores, inaccessible cavities, and catalytic pockets.  ...  This graph structure is also used to compare the dual space of a system in two different states.  ...  hisH-hisF complex, and Carl Woese for the Asp-AARS sequence alignments used in the evolutionary profiles.  ... 
doi:10.1016/j.compbiolchem.2006.01.004 pmid:16675303 fatcat:xi6ayftsnbc6jeodwpgueapbmu

Structural Genomics of Minimal Organisms and Protein Fold Space

Sung-Hou Kim, Dong Hae Shin, Jinyu Liu, Vaheh Oganesyan, Shengfeng Chen, Qian Steven Xu, Jeong-Sun Kim, Debanu Das, Ursula Schulze-Gahmen, Stephen R. Holbrook, Elizabeth L. Holbrook, Bruno A. Martinez (+15 others)
2005 Journal of Structural and Functional Genomics  
The results from the pipeline substantially increased the coverage of the protein fold space of M. pneumoniae and M. genitalium.  ...  Furthermore, about 1/2 of the structures of 'unique' protein sequences revealed new and novel folds, and over 2/3 of the structures of previously annotated 'hypothetical proteins' inferred their molecular  ...  We gratefully acknowledge the support of NIH grant GM62412 for the structures cited in this article.  ... 
doi:10.1007/s10969-005-2651-9 pmid:16211501 fatcat:ckcqooptejbzfgpng2zzrydahe

Role of a small RNA pol II subunit in TATA to transcription start site spacing

Elizabeth M. Furter-Graves, Benjamin D. Hall, Rolf Furter
1994 Nucleic Acids Research  
A point mutation in the shi gene, changing a cysteine residue in a putative zinc ribbon motif into a phenylalanine residue, was demonstrated to permit the observed usage of upstream initiation sites.  ...  The yeast shi mutation affects the spacing between the TATA promoter element and transcription initiation sites; for the H2B and ADH1 genes, a series of start sites located -50 -80 bp downstream of TATA  ...  ACKNOWLEDGEMENTS We thank T.Wallimann and H.M.Eppenberger (Cell Biology, ETH) for their most generous support towards the completion of this work.  ... 
doi:10.1093/nar/22.23.4932 pmid:7800482 pmcid:PMC523758 fatcat:tuqitlvmqfgh5oc5yb5dalvvum

How are model protein structures distributed in sequence space?

E. Bornberg-Bauer
1997 Biophysical Journal  
In analogy to protein families, nets are dense and well separated in sequence space.  ...  These graphs in sequence space are connected by point mutations and centered around prototype sequences, which tolerate the largest number (up to 55%) of neutral mutations.  ...  Applied to biopolymers, this implies that residues that are essential for function will be conserved, and others replaced in evolutionary diverse sequences.  ... 
doi:10.1016/s0006-3495(97)78268-7 pmid:9370433 pmcid:PMC1181141 fatcat:7ip6qkl6nffohcjyacgxkunuzi

RNA regulators responding to ribosomal protein S15 are frequent in sequence space

Betty L. Slinger, Michelle M. Meyer
2016 Nucleic Acids Research  
A key variable in assessing these alternatives is how frequently such regulators arise within sequence space.  ...  Subsequent footprinting and mutagenesis analysis indicates that protein binding proximal to regulatory features such as the Shine-Dalgarno sequence is sufficient to enable regulation, suggesting that regulation  ...  ACKNOWLEDGEMENTS The authors thank Arianne Babina and Daniel Beringer for their helpful comments on the manuscript.  ... 
doi:10.1093/nar/gkw754 pmid:27580716 pmcid:PMC5100602 fatcat:uul7xybd6zbb5hvszgaeaarpw4

Unsupervised statistical discovery of spaced motifs in prokaryotic genomes

Hao Tong, Paul Schliekelman, Jan Mrázek
2017 BMC Genomics  
A number of methods have been developed for discovery of such sequence motifs with a primary focus on detection of regulatory motifs and particularly transcription factor binding sites.  ...  Results: We present a novel method for detection of pairs of motifs separated by spacers of variable nucleotide sequence but conserved length.  ...  Acknowledgements Not Applicable Funding This work was supported by the grant number DBI-0950266 from the National Science Foundation Availability of data and material DNA sequences analyzed in this work  ... 
doi:10.1186/s12864-016-3400-0 pmid:28056763 pmcid:PMC5217627 fatcat:omg4zwpbcvcyvmkf76wu7ggd5m

Rapid evolution in conformational space: A study of loop regions in a ubiquitous GTP binding domain

Christian Blouin, Davin Butt, Andrew James Roger
2004 Protein Science  
We propose a model under which the diversity of protein topologies observed in these loops can be the product of a stochastic sampling of sequence and conformational space in a near-neutral fashion, while  ...  We demonstrate that these regions are self-contained and thus mostly free of the evolutionary constraints imposed by the conserved core of the domain.  ...  The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1110/ps.03299804 pmid:14978301 pmcid:PMC2286719 fatcat:r44xi3uvanh4rjz4mbhkozj7ii

MicroRNAs Responding to Space Radiation

Yujie Yan, Kunlan Zhang, Guangming Zhou, Wentao Hu
2020 International Journal of Molecular Sciences  
Compared with low-LET radiation, high-energy and high-LET radiation in space is more efficient in inducing clustered DNA damage with more serious biological consequences, such as carcinogenesis, central  ...  Space radiation also causes epigenetic changes in addition to inducing damage at the DNA level.  ...  Drosha is a conserved protein of 160 kDa size containing two series of RNase III domains (RIIIDs) and a double stranded RNA binding domain (dsRBD) [9] , which in the human body associates with DiGeorge  ... 
doi:10.3390/ijms21186603 pmid:32917057 pmcid:PMC7555309 fatcat:mp6e5wtbnjfhxhn3lhnhateyc4

Translating the Genome in Time and Space: Specialized Ribosomes, RNA Regulons, and RNA-Binding Proteins

Zhen Shi, Maria Barna
2015 Annual Review of Cell and Developmental Biology  
These hidden RNA regulons may interface with a myriad of RNA-binding proteins and specialized translation machinery to provide an additional layer of regulation to how transcripts are spatiotemporally  ...  Recent evidence shows that the ribosome itself directs how the genome is translated in time and space and reveals surprising functional specificity in individual components of the core translation machinery  ...  interacting with RNA-binding proteins (Spitale et al. 2015) .  ... 
doi:10.1146/annurev-cellbio-100814-125346 pmid:26443190 fatcat:3dbfhtfm3ncdrafxw2tud7geai
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