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Prediction of Structural Patterns of Interest from Protein Primary Sequence through Structural Alphabet: Illustration to ATP/GTP Binding Site Prediction

Christelle Reynes Leslie Regad
2015 Journal of Data Mining in Genomics & Proteomics  
The prediction of particular structural motifs associated to biological functions or to structure is of utmost importance.  ...  Then, the method ability to learn motifs corresponding to more rarely predicted functions or to other types of motifs is illustrated. Journal of  ...  This webserver allows the analysis of protein loop structures by extracting structural motifs important for both structure and function of protein.  ... 
doi:10.4172/2153-0602.1000167 fatcat:udp4qmgvcvbzdeqohbi7c2aoti

MeMotif: a database of linear motifs in α-helical transmembrane proteins

Annalisa Marsico, Kerstin Scheubert, Anne Tuukkanen, Andreas Henschel, Christof Winter, Rainer Winnenburg, Michael Schroeder
2009 Nucleic Acids Research  
Motifs contained in MeMotif can be used in different biological applications, from the identification of biochemically important functional residues which are candidates for mutagenesis experiments to  ...  Motifs are fully described in terms of several structural and functional features and editable.  ...  They further thank Loic Royer and Julia Winter for the design of the MeMotif web logo.  ... 
doi:10.1093/nar/gkp1042 pmid:19910368 pmcid:PMC2808916 fatcat:pki75wwjd5axhnkizzfcw2unni

Bioinformatic approaches for the structure and function of membrane proteins

Hyun-Jun Nam, Jou-Hyun Jeon, Sang-Uk Kim
2009 BMB Reports  
Thus, accurate prediction of membrane protein topology can increase the understanding of membrane protein function.  ...  Here, we provide a brief review of the diverse computational methods for predicting membrane protein structure and function, including recent progress and essential bioinformatics tools.  ...  Acknowledgements This work was supported by the Korea Science and Engineering Foundation grant (M10753020006-07N5302-00610 and R01-2007-000-20425-0) and the World Class University program (R31-2008-000  ... 
doi:10.5483/bmbrep.2009.42.11.697 pmid:19944009 fatcat:7rnqxfdkdjcmdhw6o5atto7iwm

Application of HMM to the Study of Three-Dimensional Protein Structure [chapter]

Christelle Reyns, Leslie Regad, Stphanie Prot, Grgory Nuel, Anne-Claude Camproux
2011 Hidden Markov Models, Theory and Applications  
Prediction of a SAH/SAM-binding site specific motif S-adenosyl-methionine (SAM) and S-adenosyl-homocysteine (SAH) are molecules associated to some methylation processes and are particularly studied in  ...  Indeed, the encoding of loop structures allowed the establishment of a systematic methodology to extract all the structural motifs of seven residues in all the loops, especially long loops.  ...  Application of HMM to the Study of Three-Dimensional Protein Structure, Hidden Markov Models, Theory and Applications, Dr.  ... 
doi:10.5772/14503 fatcat:alu7bgwfqfgrpntaoycf5o6myy

RNA structure: the long and the short of it

Stephen R Holbrook
2005 Current Opinion in Structural Biology  
At the same time, however, more detailed analysis of water, metal, ligand and protein binding to RNA is revealing the effect of these moieties on folding and structure formation.  ...  The growing database of RNA structures, coupled with efforts directed at the standardization of nomenclature and classification of motifs, has resulted in the identification and characterization of numerous  ...  Acknowledgements The author acknowledges Jasmin Yang of the NDB, and Donna Hendrix and Elizabeth Holbrook of UC Berkeley for assistance in the preparation of this manuscript.  ... 
doi:10.1016/j.sbi.2005.04.005 pmid:15963891 pmcid:PMC7127305 fatcat:lpu3srbxnvgobkv6npvdniwpii

Distant homologs of anti-apoptotic factor HAX1 encode parvalbumin-like calcium binding proteins

Katarzyna Kokoszyńska, Leszek Rychlewski, Lucjan S Wyrwicz
2010 BMC Research Notes  
Besides the general modifiers of apoptosis, several tissue-specific regulators of this process were identified including HAX1 (HS-1 associated protein X-1) -an anti-apoptotic factor active in myeloid cells  ...  link to the regulation of apoptosis.  ...  In the presented report we describe the application of several methods of homology search and protein structure prediction in drafting of hypotheses on function of HAX1.  ... 
doi:10.1186/1756-0500-3-197 pmid:20633251 pmcid:PMC2914655 fatcat:5aizkze27jhhtmi2v7nisfuwoe

IDENTIFICATION OF TRACE ELEMENT–CONTAINING PROTEINS IN GENOMIC DATABASES

Vadim N. Gladyshev, Gregory V. Kryukov, Dmitri E. Fomenko, Dolph L. Hatfield
2004 Annual review of nutrition  
STRATEGIES FOR IDENTIFICATION OF OTHER TRACE ELEMENT-ASSOCIATED PROTEINS Can one use methods developed for characterization of selenoproteomes to identify metal-containing proteins?  ...  The results of application of available PROSITE motifs and patterns for metalbinding proteins to completely sequenced genomes (D.E. Fomenko & V.N. Gladyshev, unpublished) are shown in Table 3 .  ... 
doi:10.1146/annurev.nutr.24.012003.132241 pmid:15189132 fatcat:ld4knq5dong3dnaqbucculnmci

Computational Identification of Functional Centers in Complex Proteins: A Step-by-Step Guide With Examples

Wei Zhou, Wei Chi, Wanting Shen, Wanying Dou, Junyi Wang, Xuechen Tian, Christoph Gehring, Aloysius Wong
2021 Frontiers in Bioinformatics  
In proteins, functional centers consist of the key amino acids required to perform molecular functions such as catalysis, ligand-binding, hormone- and gas-sensing.  ...  applicable for the discovery of hidden functional centers.  ...  identification of functional centers in complex proteins.  ... 
doi:10.3389/fbinf.2021.652286 fatcat:75xg2fmsdndqlbxoq7yvsu2ozi

Dark kinase annotation, mining and visualization using the Protein Kinase Ontology [article]

Saber Soleymani, Nathan Gravel, Liang-Chin Huang, Wayland Yeung, Elika Bozorgi, Nathaniel G Bendzunas, Krzysztof J Kochut, Natarajan Kannan
2022 bioRxiv   pre-print
We identify recurrent oncogenic mutations in the PAK5 activation loop predicted to alter substrate binding and phosphorylation and identify common ligand/drug binding residues in PAK family kinases, highlighting  ...  demonstrate its application in uncovering new knowledge regarding understudied members of the protein kinase family.  ...  ACKNOWLEDGEMENTS We thank members of the NK lab for feedback on the ProKinO browser and usage. FUNDING Funding from NIH (U01CA239106) is acknowledged  ... 
doi:10.1101/2022.02.25.482021 fatcat:d36wv3hcgvgsjfvxp6cweqor7a

Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs

Yutaro Kumagai, Alexis Vandenbon, Shunsuke Teraguchi, Shizuo Akira, Yutaka Suzuki
2016 BMC Genomics  
De novo structure motif prediction found a known functional motif, namely stem-loop structure containing sequence bound by RNA-binding protein Roquin and Regnase-1, as well as unknown motifs.  ...  of functional motifs.  ...  This work was supported by the Japan Society for the Promotion of Science through Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program) to Y. K., Y. S. and S.  ... 
doi:10.1186/s12864-016-3325-7 pmid:28155712 pmcid:PMC5259865 fatcat:oz5gehafarfixnmj2lzmq2ardi

Insulators in Plants: Progress and Open Questions

Amina Kurbidaeva, Michael Purugganan
2021 Genes  
In this review, we take a detailed look at known plant insulators across different species and provide an overview of potential determinants of plant insulator functions, including cis-elements and boundary  ...  The genomes of higher eukaryotes are partitioned into topologically associated domains or TADs, and insulators (also known as boundary elements) are the key elements responsible for their formation and  ...  Conflicts of Interest: The authors declare that there is no conflict of interest.  ... 
doi:10.3390/genes12091422 pmid:34573404 pmcid:PMC8470105 fatcat:g45uoehs2bbujigc537womlr5i

Therapeutic Targeting of Structural RNA Motifs in Viral RNA Genomes

Joanna Sztuba-Solinska
2014 International Journal of Virology and AIDS  
These unique structural domains, their interactions and association with host proteins and ligands, together orchestrate the multifunctionality of viral RNA genomes.  ...  identification of small molecules targeting cisacting regulatory motifs.  ... 
doi:10.23937/2469-567x/1510001 fatcat:juwhqnipffbevnugv3axw3azpe

Prediction and Experimental Detection of Structural and Functional Motifs in Intrinsically Unfolded Proteins [chapter]

Cesira de, Annalisa Pastore
2011 Selected Works in Bioinformatics  
Using ataxin-1, we retrace how the application of different bioinformatics tools has contributed to shed light on the structure and functions of the protein since its first identification.  ...  We pay particular attention to the prediction and characterization of the structural and functional features of the different protein regions and to the identification of key ELMs of crucial importance  ...  Prediction and Experimental Detection of Structural and Functional Motifs in Intrinsically Unfolded Proteins, Selected Works in Bioinformatics, Dr.  ... 
doi:10.5772/23168 fatcat:qcymlftlkzeztd4qk7sgfbkjyy

Computational Prediction of Phylogenetically Conserved Sequence Motifs for Five Different Candidate Genes in Type II Diabetic Nephropathy

T Sindhu, S Rajamanikandan, P Srinivasan
2012 Iranian Journal of Public Health  
Computational identification of phylogenetic motifs helps to understand the knowledge about known functional features that includes catalytic site, substrate binding epitopes, and protein-protein interfaces  ...  The study aimed to analyze five candidate genes involved in type II diabetic nephropathy and to predict phylogenetic motifs from their corresponding orthologous protein sequences.  ...  Acknowledgments The authors like to thank the Department of Bioinformatics, Alagappa University, Karaikudi, India for the support and providing the facilities for this work.  ... 
pmid:23113206 pmcid:PMC3469011 fatcat:6qwot7jrejcb3fu6mvang3pkcm

Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics

Lijuan Hou, Jin Xie, Yaoyao Wu, Jiaojiao Wang, Anqi Duan, Yaqi Ao, Xuejiao Liu, Xinmei Yu, Hui Yan, Jonathan Perreault, Sanshu Li
2021 BMC Genomics  
The pipeline we have established for the discovery of structured ncRNAs and the identification of their functions can also be applied to analyze other large genomes.  ...  Background Only 1.5% of the human genome encodes proteins, while large part of the remaining encodes noncoding RNAs (ncRNA). Many ncRNAs form structures and perform many important functions.  ...  Acknowledgements We would like to thank Dr. Ronald Breaker (Yale University) and Dr. Patricia Lakin-Thomas (York University, Canada) for comments and helpful suggestions.  ... 
doi:10.1186/s12864-021-07474-9 pmid:33750298 fatcat:jfxlefg345hqvc5acwlojawhfa
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