Structural biology meets data science: does anything change?
作者： Cameron Mura , Eli J Draizen , Philip E Bourne
DOI: 10.1016/J.SBI.2018.09.003
关键词: Scale (chemistry) 、 Function (engineering) 、 Visualization 、 Data science 、 Computer science 、 Software 、 Key (cryptography) 、 Digital data 、 Structure (mathematical logic) 、 Analytics
摘要: Data science has emerged from the proliferation of digital data, coupled with advances in algorithms, software and hardware (e.g., GPU computing). Innovations structural biology have been driven by similar factors, spurring us to ask: can these two fields impact one another deep hitherto unforeseen ways? We posit that answer is yes. New biological knowledge lies relationships between sequence, structure, function disease, all which play out on stage evolution, data enables elucidate at scale. Here, we consider above question five key pillars science: acquisition, engineering, analytics, visualization policy, an emphasis machine learning as premier analytics approach.
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sci-hub.se 参考文章(96)
Eugene Tseytlin, Kevin Mitchell, Elizabeth Legowski, Julia Corrigan, Girish Chavan, Rebecca S Jacobson, None, NOBLE - Flexible concept recognition for large-scale biomedical natural language processing. BMC Bioinformatics. ,vol. 17, pp. 32- 32 ,(2016) , 10.1186/S12859-015-0871-Y
Peter Cimermancic, Patrick Weinkam, T. Justin Rettenmaier, Leon Bichmann, Daniel A. Keedy, Rahel A. Woldeyes, Dina Schneidman-Duhovny, Omar N. Demerdash, Julie C. Mitchell, James A. Wells, James S. Fraser, Andrej Sali, CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. Journal of Molecular Biology. ,vol. 428, pp. 709- 719 ,(2016) , 10.1016/J.JMB.2016.01.029
Matthew D. Zimmerman, Marek Grabowski, Marcin J. Domagalski, Elizabeth M. MacLean, Maksymilian Chruszcz, Wladek Minor, Data Management in the Modern Structural Biology and Biomedical Research Environment Structural Genomics and Drug Discovery. ,vol. 1140, pp. 1- 25 ,(2014) , 10.1007/978-1-4939-0354-2_1
Zheng Zhao, Li Xie, Lei Xie, Philip E. Bourne, Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach Journal of Medicinal Chemistry. ,vol. 59, pp. 4326- 4341 ,(2016) , 10.1021/ACS.JMEDCHEM.5B02041
Erik M van Mulligen, Philippe Rocca-Serra, Maryann E Martone, Mercè Crosas, Erik A Schultes, Olivier Dumon, Morris A Swertz, Ingrid Dillo, Barend Mons, Barend Mons, Susanna-Assunta Sansone, Jeffrey S. Grethe, Jan Velterop, Scott Edmunds, Bengt L. Persson, Andra Waagmeester, Johan van der Lei, Anthony J. Brookes, Michel Dumontier, Thierry Sengstag, Jildau Bouwman, Abel L Packer, Alejandra González-Beltrán, Peter A.C ’t Hoen, Luiz Bonino da Silva Santos, Chris T. Evelo, Jaap Heringa, IJsbrand Jan Aalbersberg, Niklas Blomberg, Carole Goble, Alasdair J.G. Gray, Joost N. Kok, Richard Finkers, Philip E. Bourne, Mark Thompson, Rob W.W. Hooft, Tobias Kuhn, Jan-Willem Boiten, Paul Groth, Jun Zhao, Albert Mons, Ruben Kok, Arie Baak, Tim Clark, Gabrielle Appleton, Rene van Schaik, Mark D Wilkinson, Scott J Lusher, George Strawn, Marco Roos, Peter Wittenburg, Ted Slater, Katherine Wolstencroft, Myles Axton, The FAIR Guiding Principles for scientific data management and stewardship Scientific Data. ,vol. 3, pp. 160018- 160018 ,(2016) , 10.1038/SDATA.2016.18
Oliver Korb, Paul W Finn, Gareth Jones, The cloud and other new computational methods to improve molecular modelling. Expert Opinion on Drug Discovery. ,vol. 9, pp. 1121- 1131 ,(2014) , 10.1517/17460441.2014.941800
Anthony Ivetac, J. Andrew McCammon, Molecular recognition in the case of flexible targets. Current Pharmaceutical Design. ,vol. 17, pp. 1663- 1671 ,(2011) , 10.2174/138161211796355056
Quan Zhong, Samuel J Pevzner, Tong Hao, Yang Wang, Roberto Mosca, Jörg Menche, Mikko Taipale, Murat Taşan, Changyu Fan, Xinping Yang, Patrick Haley, Ryan R Murray, Flora Mer, Fana Gebreab, Stanley Tam, Andrew MacWilliams, Amélie Dricot, Patrick Reichert, Balaji Santhanam, Lila Ghamsari, Michael A Calderwood, Thomas Rolland, Benoit Charloteaux, Susan Lindquist, Albert‐László Barabási, David E Hill, Patrick Aloy, Michael E Cusick, Yu Xia, Frederick P Roth, Marc Vidal, An inter-species protein-protein interaction network across vast evolutionary distance. Molecular Systems Biology. ,vol. 12, pp. 865- 865 ,(2016) , 10.15252/MSB.20156484
Mathias Ferber, Jan Kosinski, Alessandro Ori, Umar J Rashid, María Moreno-Morcillo, Bernd Simon, Guillaume Bouvier, Paulo Ricardo Batista, Christoph W Müller, Martin Beck, Michael Nilges, Automated structure modeling of large protein assemblies using crosslinks as distance restraints Nature Methods. ,vol. 13, pp. 515- 520 ,(2016) , 10.1038/NMETH.3838
Emine Guven-Maiorov, Ozlem Keskin, Attila Gursoy, Carter VanWaes, Zhong Chen, Chung-Jung Tsai, Ruth Nussinov, The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway Scientific Reports. ,vol. 5, pp. 13128- 13128 ,(2015) , 10.1038/SREP13128