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Thousands of protein linear motif classes may still be undiscovered.

PloS one

Bulavka D, Aptekmann AA, Méndez NA, Krick T, Sánchez IE.
PMID: 33939703
PLoS One. 2021 May 03;16(5):e0248841. doi: 10.1371/journal.pone.0248841. eCollection 2021.

Linear motifs are short protein subsequences that mediate protein interactions. Hundreds of motif classes including thousands of motif instances are known. Our theory estimates how many motif classes remain undiscovered. As commonly done, we describe motif classes as regular...

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Bulavka D, Aptekmann AA, Méndez NA, et al. Thousands of protein linear motif classes may still be undiscovered. PLoS One. 2021;16(5):e0248841doi: 10.1371/journal.pone.0248841.
Bulavka, D., Aptekmann, A. A., Méndez, N. A., Krick, T., & Sánchez, I. E. (2021). Thousands of protein linear motif classes may still be undiscovered. PloS one, 16(5), e0248841. https://doi.org/10.1371/journal.pone.0248841
Bulavka, Denys, et al. "Thousands of protein linear motif classes may still be undiscovered." PloS one vol. 16,5 (2021): e0248841. doi: https://doi.org/10.1371/journal.pone.0248841
Bulavka D, Aptekmann AA, Méndez NA, Krick T, Sánchez IE. Thousands of protein linear motif classes may still be undiscovered. PLoS One. 2021 May 03;16(5):e0248841. doi: 10.1371/journal.pone.0248841. eCollection 2021. PMID: 33939703; PMCID: PMC8092775.
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Web server to identify similarity of amino acid motifs to compounds (SAAMCO).

Journal of chemical information and modeling

Casey FP, Davey NE, Baran I, Varekova RS, Shields DC.
PMID: 18570372
J Chem Inf Model. 2008 Jul;48(7):1524-9. doi: 10.1021/ci8000474. Epub 2008 Jun 21.

Protein-protein interactions are fundamental in mediating biological processes including metabolism, cell growth, and signaling. To be able to selectively inhibit or induce protein activity or complex formation is a key feature in controlling disease. For those situations in which...

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Casey FP, Davey NE, Baran I, et al. Web server to identify similarity of amino acid motifs to compounds (SAAMCO). J Chem Inf Model. 2008;48(7):1524-9doi: 10.1021/ci8000474.
Casey, F. P., Davey, N. E., Baran, I., Varekova, R. S., & Shields, D. C. (2008). Web server to identify similarity of amino acid motifs to compounds (SAAMCO). Journal of chemical information and modeling, 48(7), 1524-9. https://doi.org/10.1021/ci8000474
Casey, Fergal P, et al. "Web server to identify similarity of amino acid motifs to compounds (SAAMCO)." Journal of chemical information and modeling vol. 48,7 (2008): 1524-9. doi: https://doi.org/10.1021/ci8000474
Casey FP, Davey NE, Baran I, Varekova RS, Shields DC. Web server to identify similarity of amino acid motifs to compounds (SAAMCO). J Chem Inf Model. 2008 Jul;48(7):1524-9. doi: 10.1021/ci8000474. Epub 2008 Jun 21. PMID: 18570372.
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The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification.

Database : the journal of biological databases and curation

Palopoli N, Iserte JA, Chemes LB, Marino-Buslje C, Parisi G, Gibson TJ, Davey NE.
PMID: 32507889
Database (Oxford). 2020 Jan 01;2020. doi: 10.1093/database/baaa040.

Modern biology produces data at a staggering rate. Yet, much of these biological data is still isolated in the text, figures, tables and supplementary materials of articles. As a result, biological information created at great expense is significantly underutilised....

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Palopoli N, Iserte JA, Chemes LB, et al. The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. Database (Oxford). 2020;2020doi: 10.1093/database/baaa040.
Palopoli, N., Iserte, J. A., Chemes, L. B., Marino-Buslje, C., Parisi, G., Gibson, T. J., & Davey, N. E. (2020). The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. Database : the journal of biological databases and curation, 2020. https://doi.org/10.1093/database/baaa040
Palopoli, N, et al. "The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification." Database : the journal of biological databases and curation vol. 2020 (2020). doi: https://doi.org/10.1093/database/baaa040
Palopoli N, Iserte JA, Chemes LB, Marino-Buslje C, Parisi G, Gibson TJ, Davey NE. The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. Database (Oxford). 2020 Jan 01;2020. doi: 10.1093/database/baaa040. PMID: 32507889; PMCID: PMC7276420.
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Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2.

Proceedings of the National Academy of Sciences of the United States of America

Schmidt SH, Weng JH, Aoto PC, Boassa D, Mathea S, Silletti S, Hu J, Wallbott M, Komives EA, Knapp S, Herberg FW, Taylor SS.
PMID: 34088839
Proc Natl Acad Sci U S A. 2021 Jun 08;118(23). doi: 10.1073/pnas.2100844118.

To explore how pathogenic mutations of the multidomain leucine-rich repeat kinase 2 (LRRK2) hijack its finely tuned activation process and drive Parkinson's disease (PD), we used a multitiered approach. Most mutations mimic Rab-mediated activation by "unleashing" kinase activity, and...

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Schmidt SH, Weng JH, Aoto PC, et al. Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2. Proc Natl Acad Sci U S A. 2021;118(23)doi: 10.1073/pnas.2100844118.
Schmidt, S. H., Weng, J. H., Aoto, P. C., Boassa, D., Mathea, S., Silletti, S., Hu, J., Wallbott, M., Komives, E. A., Knapp, S., Herberg, F. W., & Taylor, S. S. (2021). Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2. Proceedings of the National Academy of Sciences of the United States of America, 118(23), . https://doi.org/10.1073/pnas.2100844118
Schmidt, Sven H, et al. "Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2." Proceedings of the National Academy of Sciences of the United States of America vol. 118,23 (2021). doi: https://doi.org/10.1073/pnas.2100844118
Schmidt SH, Weng JH, Aoto PC, Boassa D, Mathea S, Silletti S, Hu J, Wallbott M, Komives EA, Knapp S, Herberg FW, Taylor SS. Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2. Proc Natl Acad Sci U S A. 2021 Jun 08;118(23). doi: 10.1073/pnas.2100844118. PMID: 34088839; PMCID: PMC8201809.
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SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank.

Bioinformatics (Oxford, England)

Hugo W, Song F, Aung Z, Ng SK, Sung WK.
PMID: 20167627
Bioinformatics. 2010 Apr 15;26(8):1036-42. doi: 10.1093/bioinformatics/btq065. Epub 2010 Feb 18.

MOTIVATION: An important class of protein interactions involves the binding of a protein's domain to a short linear motif (SLiM) on its interacting partner. Extracting such motifs, either experimentally or computationally, is challenging because of their weak binding and...

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Hugo W, Song F, Aung Z, et al. SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank. Bioinformatics. 2010;26(8):1036-42doi: 10.1093/bioinformatics/btq065.
Hugo, W., Song, F., Aung, Z., Ng, S. K., & Sung, W. K. (2010). SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank. Bioinformatics (Oxford, England), 26(8), 1036-42. https://doi.org/10.1093/bioinformatics/btq065
Hugo, Willy, et al. "SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank." Bioinformatics (Oxford, England) vol. 26,8 (2010): 1036-42. doi: https://doi.org/10.1093/bioinformatics/btq065
Hugo W, Song F, Aung Z, Ng SK, Sung WK. SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank. Bioinformatics. 2010 Apr 15;26(8):1036-42. doi: 10.1093/bioinformatics/btq065. Epub 2010 Feb 18. PMID: 20167627.
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EMT-Regulome: a database for EMT-related regulatory interactions, motifs and network.

Cell death & disease

Zhao Z, Zhou W, Han Y, Peng F, Wang R, Yu R, Wang C, Liang H, Guo Z, Gu Y.
PMID: 28617437
Cell Death Dis. 2017 Jun 15;8(6):e2872. doi: 10.1038/cddis.2017.267.

No abstract available.

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Zhao Z, Zhou W, Han Y, et al. EMT-Regulome: a database for EMT-related regulatory interactions, motifs and network. Cell Death Dis. 2017;8(6):e2872doi: 10.1038/cddis.2017.267.
Zhao, Z., Zhou, W., Han, Y., Peng, F., Wang, R., Yu, R., Wang, C., Liang, H., Guo, Z., & Gu, Y. (2017). EMT-Regulome: a database for EMT-related regulatory interactions, motifs and network. Cell death & disease, 8(6), e2872. https://doi.org/10.1038/cddis.2017.267
Zhao, Zhangxiang, et al. "EMT-Regulome: a database for EMT-related regulatory interactions, motifs and network." Cell death & disease vol. 8,6 (2017): e2872. doi: https://doi.org/10.1038/cddis.2017.267
Zhao Z, Zhou W, Han Y, Peng F, Wang R, Yu R, Wang C, Liang H, Guo Z, Gu Y. EMT-Regulome: a database for EMT-related regulatory interactions, motifs and network. Cell Death Dis. 2017 Jun 15;8(6):e2872. doi: 10.1038/cddis.2017.267. PMID: 28617437; PMCID: PMC5520922.
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LMPID: a manually curated database of linear motifs mediating protein-protein interactions.

Database : the journal of biological databases and curation

Sarkar D, Jana T, Saha S.
PMID: 25776024
Database (Oxford). 2015 Mar 16;2015. doi: 10.1093/database/bav014. Print 2015.

Linear motifs (LMs), used by a subset of all protein-protein interactions (PPIs), bind to globular receptors or domains and play an important role in signaling networks. LMPID (Linear Motif mediated Protein Interaction Database) is a manually curated database which...

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Sarkar D, Jana T, Saha S. LMPID: a manually curated database of linear motifs mediating protein-protein interactions. Database (Oxford). 2015;2015doi: 10.1093/database/bav014.
Sarkar, D., Jana, T., & Saha, S. (2015). LMPID: a manually curated database of linear motifs mediating protein-protein interactions. Database : the journal of biological databases and curation, 2015. https://doi.org/10.1093/database/bav014
Sarkar, Debasree, et al. "LMPID: a manually curated database of linear motifs mediating protein-protein interactions." Database : the journal of biological databases and curation vol. 2015 (2015). doi: https://doi.org/10.1093/database/bav014
Sarkar D, Jana T, Saha S. LMPID: a manually curated database of linear motifs mediating protein-protein interactions. Database (Oxford). 2015 Mar 16;2015. doi: 10.1093/database/bav014. Print 2015. PMID: 25776024; PMCID: PMC4360622.
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SLiMScape: a protein short linear motif analysis plugin for Cytoscape.

BMC bioinformatics

O'Brien KT, Haslam NJ, Shields DC.
PMID: 23855714
BMC Bioinformatics. 2013 Jul 15;14:224. doi: 10.1186/1471-2105-14-224.

BACKGROUND: Computational protein short linear motif discovery can use protein interaction information to search for motifs among proteins which share a common interactor. Cytoscape provides a visual interface for protein networks but there is no streamlined way to rapidly...

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O'Brien KT, Haslam NJ, Shields DC. SLiMScape: a protein short linear motif analysis plugin for Cytoscape. BMC Bioinformatics. 2013;14:224doi: 10.1186/1471-2105-14-224.
O'Brien, K. T., Haslam, N. J., & Shields, D. C. (2013). SLiMScape: a protein short linear motif analysis plugin for Cytoscape. BMC bioinformatics, 14224. https://doi.org/10.1186/1471-2105-14-224
O'Brien, Kevin T, et al. "SLiMScape: a protein short linear motif analysis plugin for Cytoscape." BMC bioinformatics vol. 14 (2013): 224. doi: https://doi.org/10.1186/1471-2105-14-224
O'Brien KT, Haslam NJ, Shields DC. SLiMScape: a protein short linear motif analysis plugin for Cytoscape. BMC Bioinformatics. 2013 Jul 15;14:224. doi: 10.1186/1471-2105-14-224. PMID: 23855714; PMCID: PMC3750528.
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Showing 1 to 8 of 8 entries