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Prediction of Structural Patterns of Interest from Protein Primary Sequence through Structural Alphabet: Illustration to ATP/GTP Binding Site Prediction
2015
Journal of Data Mining in Genomics & Proteomics
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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
2009
Nucleic Acids Research
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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
2009
BMB Reports
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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]
2011
Hidden Markov Models, Theory and Applications
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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
2005
Current Opinion in Structural Biology
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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
2010
BMC Research Notes
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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
2004
Annual review of nutrition
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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
2021
Frontiers in Bioinformatics
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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]
2022
bioRxiv
pre-print
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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
2016
BMC Genomics
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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
2021
Genes
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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
2014
International Journal of Virology and AIDS
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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]
2011
Selected Works in Bioinformatics
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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
2012
Iranian Journal of Public Health
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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
2021
BMC Genomics
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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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