High-performance macromolecular data delivery and visualization for the web
Jazyk angličtina Země Spojené státy americké Médium print-electronic
Typ dokumentu časopisecké články
Grantová podpora
LM2018131
ELIXIR-CZ
CZ.02.1.01/0.0/0.0/16_013/0001777
European Regional Development Fund
PubMed
33263322
PubMed Central
PMC7709201
DOI
10.1107/s2059798320014515
PII: S2059798320014515
Knihovny.cz E-zdroje
- Klíčová slova
- browser-based, data delivery, macromolecules, visualization, web-based,
- MeSH
- internet * MeSH
- makromolekulární látky chemie MeSH
- počítačová grafika * MeSH
- software * MeSH
- uživatelské rozhraní počítače * MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- makromolekulární látky MeSH
Biomacromolecular structural data make up a vital and crucial scientific resource that has grown not only in terms of its amount but also in its size and complexity. Furthermore, these data are accompanied by large and increasing amounts of experimental data. Additionally, the macromolecular data are enriched with value-added annotations describing their biological, physicochemical and structural properties. Today, the scientific community requires fast and fully interactive web visualization to exploit this complex structural information. This article provides a survey of the available cutting-edge web services that address this challenge. Specifically, it focuses on data-delivery problems, discusses the visualization of a single structure, including experimental data and annotations, and concludes with a focus on the results of molecular-dynamics simulations and the visualization of structural ensembles.
Zobrazit více v PubMed
Abraham, M., Apostolov, R., Barnoud, J., Bauer, P., Blau, C., Bonvin, A. M. J. J., Chavent, M., Chodera, J., Čondić-Jurkić, K., Delemotte, L., Grubmüller, H., Howard, R. J., Jordan, E. J., Lindahl, E., Ollila, O. H. S., Selent, J., Smith, D. G. A., Stansfeld, P. J., Tiemann, J. K. S., Trellet, M., Woods, C. & Zhmurov, A. (2019). PubMed
Amaro, R. E. & Mulholland, A. J. (2020). PubMed
Botan, A., Favela-Rosales, F., Fuchs, P. F. J., Javanainen, M., Kanduč, M., Kulig, W., Lamberg, A., Loison, C., Lyubartsev, A., Miettinen, M. S., Monticelli, L., Määttä, J., Ollila, O. H. S., Retegan, M., Róg, T., Santuz, H. & Tynkkynen, J. (2015). PubMed PMC
Bradley, A. R., Rose, A. S., Pavelka, A., Valasatava, Y., Duarte, J. M., Prlić, A. & Rose, P. W. (2017). PubMed PMC
Carrillo-Tripp, M., Alvarez-Rivera, L., Lara-Ramírez, O. I., Becerra-Toledo, F. J., Vega-Ramírez, A., Quijas-Valades, E., González-Zavala, E., González-Vázquez, J. C., García-Vieyra, J., Santoyo-Rivera, N. B., Chapa-Vergara, S. V. & Meneses-Viveros, A. (2018). PubMed
Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., Medek, P., Biedermannova, L., Sochor, J. & Damborsky, J. (2012). PubMed PMC
Fährrolfes, R., Bietz, S., Flachsenberg, F., Meyder, A., Nittinger, E., Otto, T., Volkamer, A. & Rarey, M. (2017). PubMed PMC
Ferrara, C., Grau, S., Jäger, C., Sondermann, P., Brünker, P., Waldhauer, I., Hennig, M., Ruf, A., Rufer, A. C., Stihle, M., Umaña, P. & Benz, J. (2011). PubMed PMC
Goodsell, D. S., Zardecki, C., Di Costanzo, L., Duarte, J. M., Hudson, B. P., Persikova, I., Segura, J., Shao, C., Voigt, M., Westbrook, J. D., Young, J. Y. & Burley, S. K. (2020). PubMed PMC
Gore, S., Sanz García, E., Hendrickx, P. M. S., Gutmanas, A., Westbrook, J. D., Yang, H., Feng, Z., Baskaran, K., Berrisford, J. M., Hudson, B. P., Ikegawa, Y., Kobayashi, N., Lawson, C. L., Mading, S., Mak, L., Mukhopadhyay, A., Oldfield, T. J., Patwardhan, A., Peisach, E., Sahni, G., Sekharan, M. R., Sen, S., Shao, C., Smart, O. S., Ulrich, E. L., Yamashita, R., Quesada, M., Young, J. Y., Nakamura, H., Markley, J. L., Berman, H. M., Burley, S. K., Velankar, S. & Kleywegt, G. J. (2017).
Hanson, R. M. (2010).
Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. & Sussman, J. L. (2013).
Hoffmann, C., Centi, A., Menichetti, R. & Bereau, T. (2020). PubMed PMC
Hospital, A., Andrio, P., Cugnasco, C., Codo, L., Becerra, Y., Dans, P. D., Battistini, F., Torres, J., Goñi, R., Orozco, M. & Gelpí, J. L. (2016). PubMed PMC
Johnson, G., Autin, L., Al-Alusi, M., Goodsell, D., Sanner, M. & Olson, A. (2013
Johnson, G., Autin, L., Al-Alusi, M., Goodsell, D., Sanner, M. & Olson, A. (2013
Johnson, G., Autin, L., Al-Alusi, M., Goodsell, D., Sanner, M. & Olson, A. (2016).
Johnson, G. T., Autin, L., Al-Alusi, M., Goodsell, D. S., Sanner, M. F. & Olson, A. J. (2015). PubMed PMC
Johnson, G. T., Goodsell, D. S., Autin, L., Forli, S., Sanner, M. F. & Olson, A. J. (2014). PubMed PMC
Kim, S. J., Fernandez-Martinez, J., Nudelman, I., Shi, Y., Zhang, W., Raveh, B., Herricks, T., Slaughter, B. D., Hogan, J. A., Upla, P., Chemmama, I. E., Pellarin, R., Echeverria, I., Shivaraju, M., Chaudhury, A. S., Wang, J., Williams, R., Unruh, J. R., Greenberg, C. H., Jacobs, E. Y., Yu, Z., de la Cruz, M. J., Mironska, R., Stokes, D. L., Aitchison, J. D., Jarrold, M. F., Gerton, J. L., Ludtke, S. J., Akey, C. W., Chait, B. T., Sali, A. & Rout, M. P. (2018). PubMed PMC
Klose, T., Reteno, D. G., Benamar, S., Hollerbach, A., Colson, P., La Scola, B. & Rossmann, M. G. (2016). PubMed PMC
Martinez, X., Chavent, M. & Baaden, M. (2020). PubMed
McGibbon, R. T., Beauchamp, K. A., Harrigan, M. P., Klein, C., Swails, J. M., Hernández, C. X., Schwantes, C. R., Wang, L.-P., Lane, T. J. & Pande, V. S. (2015). PubMed PMC
Meyer, T., D’Abramo, M., Hospital, A., Rueda, M., Ferrer-Costa, C., Pérez, A., Carrillo, O., Camps, J., Fenollosa, C., Repchevsky, D., Gelpí, J. L. & Orozco, M. (2010). PubMed
Miao, H., Klein, T., Kouřil, D., Mindek, P., Schatz, K., Gröller, M. E., Kozlíková, B., Isenberg, T. & Viola, I. (2019). PubMed
PDBe-KB Consortium (2020). PubMed PMC
Pravda, L., Sehnal, D., Svobodová Vařeková, R., Navrátilová, V., Toušek, D., Berka, K., Otyepka, M. & Koča, J. (2018). PubMed PMC
Raček, T., Schindler, O., Toušek, D., Horský, V., Berka, K., Koča, J. & Svobodová, R. (2020). PubMed PMC
Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J. K. S., Aranda-García, D., Ramírez-Anguita, J. M., Stepniewski, T. M., Worp, N., Varela-Rial, A., Morales-Pastor, A., Medel-Lacruz, B., Pándy-Szekeres, G., Mayol, E., Giorgino, T., Carlsson, J., Deupi, X., Filipek, S., Filizola, M., Gómez-Tamayo, J. C., Gonzalez, A., Gutiérrez-de-Terán, H., Jiménez-Rosés, M., Jespers, W., Kapla, J., Khelashvili, G., Kolb, P., Latek, D., Marti-Solano, M., Matricon, P., Matsoukas, M.-T., Miszta, P., Olivella, M., Perez-Benito, L., Provasi, D., Ríos, S., Torrecillas, I. R., Sallander, J., Sztyler, A., Vasile, S., Weinstein, H., Zachariae, U., Hildebrand, P. W., De Fabritiis, G., Sanz, F., Gloriam, D. E., Cordomi, A., Guixà-González, R. & Selent, J. (2020).
Rose, A. S. & Hildebrand, P. W. (2015). PubMed PMC
Segura, J., Sanchez-Garcia, R., Sorzano, C. O. S. & Carazo, J. M. (2019). PubMed PMC
Sehnal, D., Deshpande, M., Vařeková, R. S., Mir, S., Berka, K., Midlik, A., Pravda, L., Velankar, S. & Koča, J. (2017). PubMed
Sehnal, D. & Grant, O. C. (2019). PubMed
Sehnal, D., Pravda, L., Svobodová Vařeková, R., Ionescu, C.-M. & Koča, J. (2015). PubMed PMC
Sehnal, D., Rose, A. S., Koča, J., Burley, S. K. & Velankar, S. (2018).
Sehnal, D., Svobodová Vařeková, R., Pravda, L., Ionescu, C.-M., Geidl, S., Horský, V., Jaiswal, D., Wimmerová, M. & Koča, J. (2015). PubMed PMC
Sirohi, D., Chen, Z., Sun, L., Klose, T., Pierson, T. C., Rossmann, M. G. & Kuhn, R. J. (2016). PubMed PMC
Tiemann, J. K. S., Guixà-González, R., Hildebrand, P. W. & Rose, A. S. (2017). PubMed
Unwin, N. (2005). PubMed
wwPDB Consortium (2019). PubMed PMC
Xu, K., Rajashankar, K. R., Chan, Y.-P., Himanen, J. P., Broder, C. C. & Nikolov, D. B. (2008). PubMed PMC
Zhao, G., Perilla, J. R., Yufenyuy, E. L., Meng, X., Chen, B., Ning, J., Ahn, J., Gronenborn, A. M., Schulten, K., Aiken, C. & Zhang, P. (2013). PubMed PMC
High-performance macromolecular data delivery and visualization for the web. Corrigendum