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Experience in testing the Motif interface

J. Su, P.R. Ritter
1991 IEEE Software  
Experience in Testing the Motif Interface ]ASON SU and PAUL R. RITTER Hewktt-Packard Interface Technology Operation knowledged as an important part of the development process.  ...  Instead, we present how testing was done in one ex-ample: the testing and quality assurance of the Open Software Foundation's Motif 1.0 graphical user-interface software.  ... 
doi:10.1109/52.73746 fatcat:wsb23iixsneunkebrw5vpbm56y

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces

Alvaro Sebastian, Bruno Contreras-Moreira
2013 Computer applications in the biosciences : CABIOS  
Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10%, 55% and 90% of the tested sequences  ...  Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity.  ...  ACKNOWLEDGEMENTS We thank our colleagues from the STREG project (L.Bülow, R.Hehl, G.Huep, B.Weisshaar, C.Dubos, L.Lepiniec and A.Koller) for their feedback and support while developing this resource.  ... 
doi:10.1093/bioinformatics/btt663 pmid:24234003 fatcat:fmfks636yrb4nm6htdx3r7gfgu

A MOTIF-BASED METHOD FOR PREDICTING INTERFACIAL RESIDUES IN BOTH THE RNA AND PROTEIN COMPONENTS OF PROTEIN-RNA COMPLEXES

Usha Muppirala, Benjamin A Lewis, Carla M Mann, Drena Dobbs
2016 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
Although the value of sequence motifs for classifying and annotating protein sequences is well established, sequence motifs have not been widely applied to predicting interfacial residues in macromolecular  ...  In 5-fold cross validation experiments, our method, PS-PRIP, achieved 92% Specificity and 61% Sensitivity, with a Matthews correlation coefficient (MCC) of 0.58 in predicting RNA-binding sites in proteins  ...  Thus, performance on the independent test set was comparable to that obtained in cross-validation experiments.  ... 
pmid:26776208 pmcid:PMC4721245 fatcat:25brj6itmjbs3axula3culacl4

A MOTIF-BASED METHOD FOR PREDICTING INTERFACIAL RESIDUES IN BOTH THE RNA AND PROTEIN COMPONENTS OF PROTEIN-RNA COMPLEXES

USHA MUPPIRALA, BENJAMIN A LEWIS, CARLA M. MANN, DRENA DOBBS
2015 Biocomputing 2016  
Although the value of sequence motifs for classifying and annotating protein sequences is well established, sequence motifs have not been widely applied to predicting interfacial residues in macromolecular  ...  Although the value of sequence motifs for classifying and annotating protein sequences is well established, sequence motifs have not been widely applied to predicting interfacial residues in macromolecular  ...  Thus, performance on the independent test set was comparable to that obtained in cross-validation experiments.  ... 
doi:10.1142/9789814749411_0041 fatcat:ojsdmqt3vzgk7pcmycrby337qu

Combinatorial multivalent interactions drive cooperative assembly of the COPII coat

Viktoriya G. Stancheva, Xiao-Han Li, Joshua Hutchings, Natalia Gomez-Navarro, Balaji Santhanam, M. Madan Babu, Giulia Zanetti, Elizabeth A. Miller
2020 Journal of Cell Biology  
The Sec31 disordered region could be replaced by evolutionarily distant sequences, suggesting plasticity in the binding interfaces.  ...  An intrinsically disordered region in the outer coat protein, Sec31, drives binding with an inner coat layer via multiple distinct interfaces, including a newly defined charge-based interaction.  ...  Acknowledgments We thank Wanda Kukulski and Manu Hegde for comments on the manuscript, Jianguo Shi for help with insect cell culture, Mark McClintock for assistance with protein purification, and David  ... 
doi:10.1083/jcb.202007135 pmid:32997735 fatcat:ciz7ud7gevhr5eiqurxcitbpa4

Prediction of RNA binding sites in proteins from amino acid sequence

M. Terribilini
2006 RNA: A publication of the RNA Society  
The availability of computational tools for predicting which residues in an RNA binding protein are likely to contact RNA should facilitate design of experiments to directly test RNA binding function and  ...  In leave-oneout cross-validation experiments, RNABindR identifies interface residues with >85% overall accuracy.  ...  likely interface residues in test sequences.  ... 
doi:10.1261/rna.2197306 pmid:16790841 pmcid:PMC1524891 fatcat:uwvrceny2ja2jowfj7qc3bvfiy

Effects of search pattern variations in motif discovery algorithm: MotifFinder

William H.P. Leung, Wai Chi Tam, Bill C.H. Chang, Saman K. Halgamuge
2003 IFAC Proceedings Volumes  
In this study, a recently proposed motif discovery algorithm is implemented with improved computational efficiency.  ...  The obtained characteristics can then be used to further improve the capability and accuracy of the protein motif discovery algorithm.  ...  in the display area of the interface.  ... 
doi:10.1016/s1474-6670(17)33554-1 fatcat:n7dun6ksezh7hhq3y7zfjyr7je

CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events

Giovanni Scala, Antonio Federico, Dario Greco
2021 BMC Bioinformatics  
Research in this field still lacks a qualitative perspective, linked to the identification of certain sequences (or DNA motifs) related to particular DNA methylation phenomena.  ...  This aspect has been previously characterized in a quantitative manner by inspecting the nucleotidic composition in the region.  ...  Acknowledgements The authors are grateful to Troy Faithfull for his critical comments on the manuscript.  ... 
doi:10.1186/s12859-021-04191-8 pmid:34039269 fatcat:v3fnjszjvbbchdtdarmua7wwre

A sequence-specific transcription activator motif and powerful synthetic variants that bind Mediator using a fuzzy protein interface

L. Warfield, L. M. Tuttle, D. Pacheco, R. E. Klevit, S. Hahn
2014 Proceedings of the National Academy of Sciences of the United States of America  
Our results suggest a mechanism to explain how a subset of natural activators use redundant sequence motifs and great flexibility in the binding interface to target unrelated coactivators.  ...  The additional hydrophobic residues in the synthetic ADs likely allow multiple faces of the AD helix to interact with the Gal11 activator-binding domain, effectively forming a fuzzier interface than that  ...  Petesch for sequence analysis of AD motifs and communication of unpublished results; and J.  ... 
doi:10.1073/pnas.1412088111 pmid:25122681 pmcid:PMC4151740 fatcat:dodave3qpbfqtcwrweqilsufjm

SLiMScape: a protein short linear motif analysis plugin for Cytoscape

Kevin T O'Brien, Niall J Haslam, Denis C Shields
2013 BMC Bioinformatics  
This significantly aids in the discovery of novel short linear motifs and in visualizing the distribution of known motifs.  ...  Cytoscape provides a visual interface for protein networks but there is no streamlined way to rapidly visualize motifs in a network of proteins, or to integrate computational discovery with such visualizations  ...  Acknowledgements This work was supported by The Irish Research Council for Science, Engineering and Technology [IRCSET] and the UCD Bioinformatics and Systems Biology PhD Programme.  ... 
doi:10.1186/1471-2105-14-224 pmid:23855714 pmcid:PMC3750528 fatcat:fwu4tyu55vfdrcms5wavupfpgy

Improved Modeling of Side-Chain–Base Interactions and Plasticity in Protein–DNA Interface Design

Summer B. Thyme, David Baker, Philip Bradley
2012 Journal of Molecular Biology  
To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein-DNA interface and found that many positions tolerated multiple amino acids.  ...  This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model.  ...  in Global Health Initiative, and the Howard Hughes Medical Institute.  ... 
doi:10.1016/j.jmb.2012.03.005 pmid:22426128 pmcid:PMC3566986 fatcat:ccsziyxznbd4dej436x5uoqw7q

Viral Determinants of Polarized Assembly for the Murine Leukemia Virus

J. Jin, F. Li, W. Mothes
2011 Journal of Virology  
interface.  ...  We present here the viral determinants in the Env cytoplasmic tail and Gag that are important in this process.  ...  This study is supported by the NIH R01 CA098727 to W.M. and a fellowship from amfAR, the Foundation for AIDS Research, to J.J.  ... 
doi:10.1128/jvi.00409-11 pmid:21593177 pmcid:PMC3147905 fatcat:nwwwt2dr3jd55eaq33cw7i6gsy

Structural Analysis of the Interaction between Dishevelled2 and Clathrin AP-2 Adaptor, A Critical Step in Noncanonical Wnt Signaling

Anan Yu, Yi Xing, Stephen C. Harrison, Tomas Kirchhausen
2010 Structure  
Mutation of residues at the DEP-m2 contact or in the tyrosine motif reduce affinity of Dvl2 for m2 and block efficient internalization of Fz4 in response to ligation by Wnt5a.  ...  This domain:domain interface shows that parts of the m2 surface distinct from the tyrosine-motif site can help recruit specific receptors or adaptors into a clathrin coated pit.  ...  S.C.H. is an Investigator in the Howard Hughes Medical Institute.  ... 
doi:10.1016/j.str.2010.07.010 pmid:20947020 pmcid:PMC2992793 fatcat:a67g47rvx5fehkcy3jqaj3ocji

Contextual Specificity in Peptide-Mediated Protein Interactions

Amelie Stein, Patrick Aloy, Lennart Randau
2008 PLoS ONE  
We also studied and quantified the topological and energetic variability of interaction interfaces, finding a much higher heterogeneity in the context residues than in the consensus binding motifs.  ...  motif (i.e. the context).  ...  It is worth remembering that, in this experiment, we tested only possible cases of potential cross-reaction between protein pairs of known 3D structure within species, regardless of other key aspects in  ... 
doi:10.1371/journal.pone.0002524 pmid:18596940 pmcid:PMC2438476 fatcat:5ccikd2ztfg3vhssafct2f3nui

Interface Similarity Improves Comparison of DNA-Binding Proteins: The Homeobox Example [chapter]

Álvaro Sebastián, Carlos P. Cantalapiedra, Bruno Contreras-Moreira
2012 Lecture Notes in Computer Science  
proteins might bind to the same DNA motif.  ...  Here we take the complete set of Homeobox proteins from Drosophila melanogaster and their preferred DNA motifs, which would fall in the largest 3D-footprint superfamily and were recently characterized  ...  A receiver operating characteristic (ROC) curve was also plotted taking as truth test a motif similarity score ≥ 5 .  ... 
doi:10.1007/978-3-642-28062-7_8 fatcat:taow7ed2pvgohg5kmp7gwe534u
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