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Showing 13 to 18 of 18 entries
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Recognition of LD motifs by the focal adhesion targeting domains of focal adhesion kinase and proline-rich tyrosine kinase 2-beta: Insights from molecular dynamics simulations.

Proteins

Michael E, Polydorides S, Promponas VJ, Skourides P, Archontis G.
PMID: 32776636
Proteins. 2020 Aug 10; doi: 10.1002/prot.25992. Epub 2020 Aug 10.

The focal adhesion kinase (FAK) and the proline-rich tyrosine kinase 2-beta (PYK2) are implicated in cancer progression and metastasis and represent promising biomarkers and targets for cancer therapy. FAK and PYK2 are recruited to focal adhesions (FAs) via interactions...

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Michael E, Polydorides S, Promponas VJ, et al. Recognition of LD motifs by the focal adhesion targeting domains of focal adhesion kinase and proline-rich tyrosine kinase 2-beta: Insights from molecular dynamics simulations. Proteins. 2020;doi: 10.1002/prot.25992.
Michael, E., Polydorides, S., Promponas, V. J., Skourides, P., & Archontis, G. (2020). Recognition of LD motifs by the focal adhesion targeting domains of focal adhesion kinase and proline-rich tyrosine kinase 2-beta: Insights from molecular dynamics simulations. Proteins, . https://doi.org/10.1002/prot.25992
Michael, Eleni, et al. "Recognition of LD motifs by the focal adhesion targeting domains of focal adhesion kinase and proline-rich tyrosine kinase 2-beta: Insights from molecular dynamics simulations." Proteins vol. (2020). doi: https://doi.org/10.1002/prot.25992
Michael E, Polydorides S, Promponas VJ, Skourides P, Archontis G. Recognition of LD motifs by the focal adhesion targeting domains of focal adhesion kinase and proline-rich tyrosine kinase 2-beta: Insights from molecular dynamics simulations. Proteins. 2020 Aug 10; doi: 10.1002/prot.25992. Epub 2020 Aug 10. PMID: 32776636.
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An intrinsically disordered proteins community for ELIXIR.

F1000Research

Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE.
PMID: 31824649
F1000Res. 2019 Oct 15;8. doi: 10.12688/f1000research.20136.1. eCollection 2019.

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The...

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Davey NE, Babu MM, Blackledge M, et al. An intrinsically disordered proteins community for ELIXIR. F1000Res. 2019;8doi: 10.12688/f1000research.20136.1.
Davey, N. E., Babu, M. M., Blackledge, M., Bridge, A., Capella-Gutierrez, S., Dosztanyi, Z., Drysdale, R., Edwards, R. J., Elofsson, A., Felli, I. C., Gibson, T. J., Gutmanas, A., Hancock, J. M., Harrow, J., Higgins, D., Jeffries, C. M., Le Mercier, P., Mészáros, B., Necci, M., Notredame, C., Orchard, S., Ouzounis, C. A., Pancsa, R., Papaleo, E., Pierattelli, R., Piovesan, D., Promponas, V. J., Ruch, P., Rustici, G., Romero, P., Sarntivijai, S., Saunders, G., Schuler, B., Sharan, M., Shields, D. C., Sussman, J. L., Tedds, J. A., Tompa, P., Turewicz, M., Vondrasek, J., Vranken, W. F., Wallace, B. A., Wichapong, K., & Tosatto, S. C. E. (2019). An intrinsically disordered proteins community for ELIXIR. F1000Research, 8. https://doi.org/10.12688/f1000research.20136.1
Davey, Norman E, et al. "An intrinsically disordered proteins community for ELIXIR." F1000Research vol. 8 (2019). doi: https://doi.org/10.12688/f1000research.20136.1
Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE. An intrinsically disordered proteins community for ELIXIR. F1000Res. 2019 Oct 15;8. doi: 10.12688/f1000research.20136.1. eCollection 2019. PMID: 31824649; PMCID: PMC6880265.
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Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure.

Standards in genomic sciences

Promponas VJ, Iliopoulos I, Ouzounis CA.
PMID: 26594309
Stand Genomic Sci. 2015 Nov 19;10:108. doi: 10.1186/s40793-015-0101-2. eCollection 2015.

The function annotation process in computational biology has increasingly shifted from the traditional characterization of individual biochemical roles of protein molecules to the system-wide detection of entire metabolic pathways and genomic structures. The so-called genome-aware methods broaden misannotation inconsistencies...

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Promponas VJ, Iliopoulos I, Ouzounis CA. Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure. Stand Genomic Sci. 2015;10:108doi: 10.1186/s40793-015-0101-2.
Promponas, V. J., Iliopoulos, I., & Ouzounis, C. A. (2015). Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure. Standards in genomic sciences, 10108. https://doi.org/10.1186/s40793-015-0101-2
Promponas, Vasilis J, et al. "Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure." Standards in genomic sciences vol. 10 (2015): 108. doi: https://doi.org/10.1186/s40793-015-0101-2
Promponas VJ, Iliopoulos I, Ouzounis CA. Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure. Stand Genomic Sci. 2015 Nov 19;10:108. doi: 10.1186/s40793-015-0101-2. eCollection 2015. PMID: 26594309; PMCID: PMC4653902.
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DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.

Nucleic acids research

Quaglia F, Mészáros B, Salladini E, Hatos A, Pancsa R, Chemes LB, Pajkos M, Lazar T, Peña-Díaz S, Santos J, Ács V, Farahi N, Fichó E, Aspromonte MC, Bassot C, Chasapi A, Davey NE, Davidović R, Dobson L, Elofsson A, Erdős G, Gaudet P, Giglio M, Glavina J, Iserte J, Iglesias V, Kálmán Z, Lambrughi M, Leonardi E, Longhi S, Macedo-Ribeiro S, Maiani E, Marchetti J, Marino-Buslje C, Mészáros A, Monzon AM, Minervini G, Nadendla S, Nilsson JF, Novotný M, Ouzounis CA, Palopoli N, Papaleo E, Pereira PJB, Pozzati G, Promponas VJ, Pujols J, Rocha ACS, Salas M, Sawicki LR, Schad E, Shenoy A, Szaniszló T, Tsirigos KD, Veljkovic N, Parisi G, Ventura S, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D.
PMID: 34850135
Nucleic Acids Res. 2022 Jan 07;50:D480-D487. doi: 10.1093/nar/gkab1082.

The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web...

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Quaglia F, Mészáros B, Salladini E, et al. DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Res. 2022;50:D480-D487doi: 10.1093/nar/gkab1082.
Quaglia, F., Mészáros, B., Salladini, E., Hatos, A., Pancsa, R., Chemes, L. B., Pajkos, M., Lazar, T., Peña-Díaz, S., Santos, J., Ács, V., Farahi, N., Fichó, E., Aspromonte, M. C., Bassot, C., Chasapi, A., Davey, N. E., Davidović, R., Dobson, L., Elofsson, A., Erdős, G., Gaudet, P., Giglio, M., Glavina, J., Iserte, J., Iglesias, V., Kálmán, Z., Lambrughi, M., Leonardi, E., Longhi, S., Macedo-Ribeiro, S., Maiani, E., Marchetti, J., Marino-Buslje, C., Mészáros, A., Monzon, A. M., Minervini, G., Nadendla, S., Nilsson, J. F., Novotný, M., Ouzounis, C. A., Palopoli, N., Papaleo, E., Pereira, P. J. B., Pozzati, G., Promponas, V. J., Pujols, J., Rocha, A. C. S., Salas, M., Sawicki, L. R., Schad, E., Shenoy, A., Szaniszló, T., Tsirigos, K. D., Veljkovic, N., Parisi, G., Ventura, S., Dosztányi, Z., Tompa, P., Tosatto, S. C. E., & Piovesan, D. (2022). DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic acids research, 50D480-D487. https://doi.org/10.1093/nar/gkab1082
Quaglia, Federica, et al. "DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation." Nucleic acids research vol. 50 (2022): D480-D487. doi: https://doi.org/10.1093/nar/gkab1082
Quaglia F, Mészáros B, Salladini E, Hatos A, Pancsa R, Chemes LB, Pajkos M, Lazar T, Peña-Díaz S, Santos J, Ács V, Farahi N, Fichó E, Aspromonte MC, Bassot C, Chasapi A, Davey NE, Davidović R, Dobson L, Elofsson A, Erdős G, Gaudet P, Giglio M, Glavina J, Iserte J, Iglesias V, Kálmán Z, Lambrughi M, Leonardi E, Longhi S, Macedo-Ribeiro S, Maiani E, Marchetti J, Marino-Buslje C, Mészáros A, Monzon AM, Minervini G, Nadendla S, Nilsson JF, Novotný M, Ouzounis CA, Palopoli N, Papaleo E, Pereira PJB, Pozzati G, Promponas VJ, Pujols J, Rocha ACS, Salas M, Sawicki LR, Schad E, Shenoy A, Szaniszló T, Tsirigos KD, Veljkovic N, Parisi G, Ventura S, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Res. 2022 Jan 07;50:D480-D487. doi: 10.1093/nar/gkab1082. PMID: 34850135.
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Active Surveillance-Is It Feasible for Intermediate-risk Localised Prostate Cancer?.

European urology open science

Mukherjee S, Promponas I, Petrides N, Hossain D, Abbaraju J, Madaan S.
PMID: 34337491
Eur Urol Open Sci. 2021 Jan 08;24:17-24. doi: 10.1016/j.euros.2020.12.005. eCollection 2021 Feb.

BACKGROUND: Although active surveillance (AS) is a well-recognised treatment option for localised low-risk prostate cancer (LRPC), its role in the management of localised intermediate-risk prostate cancer (IRPC) is not clear yet and the available literature is slightly contradictory.OBJECTIVE: To...

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Mukherjee S, Promponas I, Petrides N, et al. Active Surveillance-Is It Feasible for Intermediate-risk Localised Prostate Cancer?. Eur Urol Open Sci. 2021;24:17-24doi: 10.1016/j.euros.2020.12.005.
Mukherjee, S., Promponas, I., Petrides, N., Hossain, D., Abbaraju, J., & Madaan, S. (2021). Active Surveillance-Is It Feasible for Intermediate-risk Localised Prostate Cancer?. European urology open science, 2417-24. https://doi.org/10.1016/j.euros.2020.12.005
Mukherjee, Subhabrata, et al. "Active Surveillance-Is It Feasible for Intermediate-risk Localised Prostate Cancer?." European urology open science vol. 24 (2021): 17-24. doi: https://doi.org/10.1016/j.euros.2020.12.005
Mukherjee S, Promponas I, Petrides N, Hossain D, Abbaraju J, Madaan S. Active Surveillance-Is It Feasible for Intermediate-risk Localised Prostate Cancer?. Eur Urol Open Sci. 2021 Jan 08;24:17-24. doi: 10.1016/j.euros.2020.12.005. eCollection 2021 Feb. PMID: 34337491; PMCID: PMC8317861.
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DisProt: intrinsic protein disorder annotation in 2020.

Nucleic acids research

Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, Iglesias V, Kajava AV, Kovacs OP, Lamb J, Lambrughi M, Lazar T, Leclercq JY, Leonardi E, Macedo-Ribeiro S, Macossay-Castillo M, Maiani E, Manso JA, Marino-Buslje C, Martínez-Pérez E, Mészáros B, Mičetić I, Minervini G, Murvai N, Necci M, Ouzounis CA, Pajkos M, Paladin L, Pancsa R, Papaleo E, Parisi G, Pasche E, Barbosa Pereira PJ, Promponas VJ, Pujols J, Quaglia F, Ruch P, Salvatore M, Schad E, Szabo B, Szaniszló T, Tamana S, Tantos A, Veljkovic N, Ventura S, Vranken W, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D.
PMID: 31713636
Nucleic Acids Res. 2020 Jan 08;48:D269-D276. doi: 10.1093/nar/gkz975.

The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements...

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Hatos A, Hajdu-Soltész B, Monzon AM, et al. DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res. 2020;48:D269-D276doi: 10.1093/nar/gkz975.
Hatos, A., Hajdu-Soltész, B., Monzon, A. M., Palopoli, N., Álvarez, L., Aykac-Fas, B., Bassot, C., Benítez, G. I., Bevilacqua, M., Chasapi, A., Chemes, L., Davey, N. E., Davidović, R., Dunker, A. K., Elofsson, A., Gobeill, J., Foutel, N. S. G., Sudha, G., Guharoy, M., Horvath, T., Iglesias, V., Kajava, A. V., Kovacs, O. P., Lamb, J., Lambrughi, M., Lazar, T., Leclercq, J. Y., Leonardi, E., Macedo-Ribeiro, S., Macossay-Castillo, M., Maiani, E., Manso, J. A., Marino-Buslje, C., Martínez-Pérez, E., Mészáros, B., Mičetić, I., Minervini, G., Murvai, N., Necci, M., Ouzounis, C. A., Pajkos, M., Paladin, L., Pancsa, R., Papaleo, E., Parisi, G., Pasche, E., Barbosa Pereira, P. J., Promponas, V. J., Pujols, J., Quaglia, F., Ruch, P., Salvatore, M., Schad, E., Szabo, B., Szaniszló, T., Tamana, S., Tantos, A., Veljkovic, N., Ventura, S., Vranken, W., Dosztányi, Z., Tompa, P., Tosatto, S. C. E., & Piovesan, D. (2020). DisProt: intrinsic protein disorder annotation in 2020. Nucleic acids research, 48D269-D276. https://doi.org/10.1093/nar/gkz975
Hatos, András, et al. "DisProt: intrinsic protein disorder annotation in 2020." Nucleic acids research vol. 48 (2020): D269-D276. doi: https://doi.org/10.1093/nar/gkz975
Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, Iglesias V, Kajava AV, Kovacs OP, Lamb J, Lambrughi M, Lazar T, Leclercq JY, Leonardi E, Macedo-Ribeiro S, Macossay-Castillo M, Maiani E, Manso JA, Marino-Buslje C, Martínez-Pérez E, Mészáros B, Mičetić I, Minervini G, Murvai N, Necci M, Ouzounis CA, Pajkos M, Paladin L, Pancsa R, Papaleo E, Parisi G, Pasche E, Barbosa Pereira PJ, Promponas VJ, Pujols J, Quaglia F, Ruch P, Salvatore M, Schad E, Szabo B, Szaniszló T, Tamana S, Tantos A, Veljkovic N, Ventura S, Vranken W, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res. 2020 Jan 08;48:D269-D276. doi: 10.1093/nar/gkz975. PMID: 31713636; PMCID: PMC7145575.
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Showing 13 to 18 of 18 entries