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Identifying protein function and functional links based on large-scale co-occurrence patterns

Zohar Pasternak, Noam Chapnik, Roy Yosef, Naama M. Kopelman, Edouard Jurkevitch, Elad Segev, Yanbin Yin
2022 PLoS ONE  
In order to decipher protein function and examine functional associations, we developed "Cliquely", a software tool based on the exploration of co-occurrence patterns.  ...  Users can employ the tool to explore co-occurrence networks using a protein of interest and a customizable level of stringency, either for the entire dataset or for a one of the three domains—Archaea,  ...  One of the approaches that are based on this principle is termed phylogenetic profiling, a method which is based on the assumption that genes that are functionally related will be characterized by similar  ... 
doi:10.1371/journal.pone.0264765 pmid:35239724 pmcid:PMC8893610 fatcat:aekiv2teo5fsvkp74zmk7gtvrm

Automatic Identification of Highly Conserved Family Regions and Relationships in Genome Wide Datasets Including Remote Protein Sequences

Tunca Doğan, Bilge Karaçalı, Vladimir N. Uversky
2013 PLoS ONE  
reveal previously unknown protein families as well as new members to existing ones.  ...  We have then applied the proposed method to a genome wide dataset of 17793 human proteins and generated a global association map to each of the 4753 identified conserved regions.  ...  Conceived and designed the experiments: TD BK. Performed the experiments: TD. Analyzed the data: TD BK. Contributed reagents/ materials/analysis tools: TD BK. Wrote the paper: TD.  ... 
doi:10.1371/journal.pone.0075458 pmid:24069417 pmcid:PMC3771926 fatcat:l3jidf776raxfayidnzjschr24

Towards Site-Based Protein Functional Annotations

Seak Fei Lei, Jun Huan
2008 2008 IEEE International Conference on Bioinformatics and Biomedicine  
To improve the functional prediction ability based on the local protein structures, we proposed three different methods. 1) We used statistical model (known as Markov Random Field) to describe protein  ...  active region based on the structure motifs. 2) We developd a filter that considers the local environment around the active sites to remove the false positives. 3) we created multiple structure motifs  ...  Given an active site from a protein family and a protein structure, graph matching determines whether an one-to-one mapping function exists between them.  ... 
doi:10.1109/bibm.2008.58 dblp:conf/bibm/LeiH08 fatcat:mslwachpg5gtbcblvycxgguwdy

Towards site-based protein functional annotations

Seak Fei Lei, Jun Huan
2010 International Journal of Data Mining and Bioinformatics  
To improve the functional prediction ability based on the local protein structures, we proposed three different methods. 1) We used statistical model (known as Markov Random Field) to describe protein  ...  active region based on the structure motifs. 2) We developd a filter that considers the local environment around the active sites to remove the false positives. 3) we created multiple structure motifs  ...  Given an active site from a protein family and a protein structure, graph matching determines whether an one-to-one mapping function exists between them.  ... 
doi:10.1504/ijdmb.2010.034200 pmid:20815142 pmcid:PMC2936724 fatcat:uyx5m4lvl5dnzgok4l72xkmivu

Evaluation and improvements of clustering algorithms for detecting remote homologous protein families

Juliana S Bernardes, Fabio RJ Vieira, Lygia MM Costa, Gerson Zaverucha
2015 BMC Bioinformatics  
and a novel measure based on profile-profile comparisons, used here for the first time.  ...  To the best of our knowledge, a systematic evaluation of clustering methods over distant homologous proteins is still lacking.  ...  , and several universities as well as other funding bodies (see https://www.grid5000.fr).  ... 
doi:10.1186/s12859-014-0445-4 pmid:25651949 pmcid:PMC4339679 fatcat:3m3hi6zb6fepjfp33u6m6ra4ru

Quantifying the Similarities within Fold Space

Andrew Harrison, Frances Pearl, Richard Mott, Janet Thornton, Christine Orengo
2002 Journal of Molecular Biology  
We have used GRATH, a graph-based structure comparison algorithm, to map the similarities between the different folds observed in the CATH domain structure database.  ...  Apart from one example, all the most gregarious folds matching 20% or more of the other folds in the database, are ab proteins.  ...  Acknowledgements We are very grateful to and thank: Ram Samudrala for providing a copy of the Bron-Kerbosch algorithm in C through the Internet; Jonathan Barker for discussions about the statistical issues  ... 
doi:10.1016/s0022-2836(02)00992-0 pmid:12417203 fatcat:wnybwphkrjg63gvmnlvtfwf2nu

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development

Deepak Bandyopadhyay, Jun Huan, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha
2009 Journal of Computer-Aided Molecular Design  
We present a novel automated protein structure-based function prediction method using libraries of local residue packing patterns that are common to most proteins in a known functional family.  ...  This method can assign a new structure to a specific functional family in cases where sequence alignments, sequence patterns, structural superposition and active site templates fail to provide accurate  ...  Acknowledgments These studies were supported by NIH grant GM068665 and NSF grant CCF-0523875.  ... 
doi:10.1007/s10822-009-9273-4 pmid:19543979 fatcat:4dgs7ziwmjdhtiizotrjy6f4r4

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family

R. J. Najmanovich, A. Allali-Hassani, R. J. Morris, L. Dombrovsky, P. W. Pan, M. Vedadi, A. N. Plotnikov, A. Edwards, C. Arrowsmith, J. M. Thornton
2007 Bioinformatics  
Results: The comparison of binding site structural similarities and small-molecule binding profiles shows that proteins with similar small-molecule binding profiles tend to have a higher degree of binding  ...  family correlate with small-molecule binding profiles.  ...  Genomics Institute, GlaxoSmithKline, the Ontario Innovation Trust, the Ontario Research and Development Challenge Fund and the Wellcome Trust.  ... 
doi:10.1093/bioinformatics/btl292 pmid:17237076 fatcat:nlxw2h2vgffqxplixchlnrhqii

Multiple domain protein diagnostic patterns

R. Mark Adams, Sudeshna Das, Temple F. Smith
1996 Protein Science  
Our algorithm was applied to sequences gathered using a variety of methods, including BLAST, common keywords, and common E.C. numbers.  ...  Patterns generated from a large number of sequence families were analyzed for probable multiple-domain structure.  ...  This work was supported in part by grant #P41 LM05205-12 from the National Library of Medicine and a grant from INCYTE Pharmaceuticals, Inc.  ... 
doi:10.1002/pro.5560050703 pmid:8819157 pmcid:PMC2143450 fatcat:fhhwlyoszbewxldk6uk4xkfucq

How to Measure the Similarity Between Protein Ligand-Binding Sites?

Esther Kellenberger, Claire Schalon, Didier Rognan
2008 Current Computer - Aided Drug Design  
Over the last ten years, several computational methods were proposed, mostly based on geometrical comparisons.  ...  , comparison of binding sites across a functional family, comparison of homology models, database screening.  ...  This assumption was later supported by the structural determination of the homologous protein MshB.  ... 
doi:10.2174/157340908785747401 fatcat:yhbu4ge3evftfcxgrleqzoh55m

An Integrated Approach (CLuster Analysis Integration Method) to Combine Expression Data and Protein–Protein Interaction Networks in Agrigenomics: Application on Arabidopsis thaliana

Daniele Santoni, Aleksandra Swiercz, Agnieszka Żmieńko, Marta Kasprzak, Marek Blazewicz, Paola Bertolazzi, Giovanni Felici
2014 Omics  
CLAIM is based on the separate clustering of MA and PPI data; the clusters are merged in a special graph; cliques of this graph are subsets of strongly connected proteins.  ...  We propose a new method to integrate co-expression data obtained through DNA microarray analysis (MA) and protein-protein interaction (PPI) network data, and apply it to Arabidopsis thaliana.  ...  and their analysis (www.ncn.gov.pl); the FLAGSHIP "InterOmics" project (PB.P05) funded by the Italian MIUR and CNR institutions supported the work on method design and testing (www.cnr.it).  ... 
doi:10.1089/omi.2013.0050 pmid:24404838 pmcid:PMC3920845 fatcat:7nemcn4omnbjnf2bjljslfkfgq

SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification

Ming Fan, Ka-Chun Wong, Taewoo Ryu, Timothy Ravasi, Xin Gao, Annalisa Pastore
2012 PLoS ONE  
Local similarity can thus be detected and encoded into a graph structure, in which each node represents a protein sequence and each edge weight represents the shared hash seeds between the two nodes.  ...  Traditional database-based domain prediction methods cannot identify novel domains, however, and alignment-based methods, which look for recurring segments in the proteome, are computationally demanding  ...  Acknowledgments We are grateful to Ming Li for fruitful discussions. We thank Virginia Unkefer for editorial work on the manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0039475 pmid:22761802 pmcid:PMC3386278 fatcat:6szpfrjlijdz5eh4ltx7y2hh4e

IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities

Natalja Kurbatova, Matthieu Chartier, María Inés Zylber, Rafael Najmanovich
2013 F1000Research  
IsoCleft Finder is a web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule  ...  This interface permits the visualization of target ligands superimposed on the query cavity and additionally provides a table of pairwise ligand topological similarities.  ...  These include, among others, global structural (fold) similarity, various sequence and sequence-profile based similarity methods, reverse templates and genome co-localization.  ... 
doi:10.12688/f1000research.2-117.v2 pmid:24555058 pmcid:PMC3892921 fatcat:o3bojnp6evdwtcqm2pzy3bue5y

Discovering non-coding RNA elements in Drosophila 3' untranslated regions

Cuncong Zhong, Justen Andrews, Shaojie Zhang
2014 International Journal of Bioinformatics Research and Applications  
Many of the regulations are found to be triggered by RNA-protein or RNA-RNA interaction, which usually occurs in the 3′ Untranslated Regions (3′-UTRs) of the mRNA (Besse and Ephrussi,  ...  One of these clusters corresponds to genes that are preferentially expressed in male Drosophila.  ...  His research is focused on bioinformatics, which includes ncRNA gene finding, RNA analysis, and computational genomics.  ... 
doi:10.1504/ijbra.2014.062996 pmid:24989864 pmcid:PMC4121059 fatcat:gi7zidz6qvaerp2sot36wmw73a

Graph pyramids for protein function prediction

Tushar Sandhan, Youngjun Yoo, Jin Young Choi, Sun Kim
2015 BMC Medical Genomics  
As proteins from the same family exhibit similar characteristics, homology based approaches predict protein functions via protein classification.  ...  Different underlying properties of the protein families are uncovered by operating the proposed graph based features at various pyramid levels.  ...  So an approach based on protein homology is a fast, approximate and a primary way used to tackle such a daunting task of protein function prediction.  ... 
doi:10.1186/1755-8794-8-s2-s12 pmid:26044522 pmcid:PMC4460595 fatcat:qdhmmaf7s5bubcsczljvxn77ny
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