XXV General Assembly and Congress of the
International Union of Crystallography - IUCr 2021
August 14 - 22, 2021 | Prague, Czech Republic
Conference Agenda
Overview and details of the sessions of this conference. Please select a date or location to show only sessions at that day or location. Please select a single session for detailed view (with abstracts and downloads if available).
Please note that all times are shown in the time zone of the conference. The current conference time is: 19th Apr 2024, 10:17:59am CEST
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Session Overview |
| Session | ||
MS-1: Structural bioinformatics
Invited: Zhichao Miao (UK) | ||
| Session Abstract | ||
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For all abstracts of the session as prepared for Acta Crystallographica see PDF in Introduction, or individual abstracts below. | ||
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10:20am - 10:25am
ID: 1728 / MS-1: 1 Introduction Oral/poster Introduction to session 10:25am - 10:55am
ID: 580 / MS-1: 2 Bursary application Invited lecture to session MS: Structural bioinformatics, Structural bioinformatics Keywords: RNA, structure prediction, RNA-Puzzles, Assessment, viral RNA RNA-Puzzles - the evaluation and automation of RNA 3D structure prediction 1Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China; 2Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; 3European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK Bibliography
Zhichao Miao, Pablo Moreno, Ni Huang, Irene Papatheodorou, Alvis Brazma, Sarah A Teichmann. Putative cell type discovery from single-cell gene expression data. Nature Methods (in press) Magnus, M., Antczak, M., Zok, T., Wiedemann, J., Lukasiak, P., Cao, Y., Bujnicki, J. M., Westhof, E., Szachniuk, M. & Miao, Z. RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Nucleic Acids Res. 48, 576–588 (2020). (corresponding author) Popescu, Dorin-Mirel, Rachel A. Botting, Emily Stephenson, Kile Green, Simone Webb, Laura Jardine, Emily F. Calderbank, et al. 2019. “Decoding Human Fetal Liver Haematopoiesis.” Nature 574 (7778): 365–71. Polański, Krzysztof, Jong-Eun Park, Matthew D. Young, Zhichao Miao, Kerstin B. Meyer, and Sarah A. Teichmann. 2019. “BBKNN: Fast Batch Alignment of Single Cell Transcriptomes.” Bioinformatics , August. https://doi.org/10.1093/bioinformatics/btz625. Lei Li1^, Shuang Chen^, Zhichao Miao^, et al. (2019) AbRSA: A robust tool for antibody numbering. Protein Science doi:10.1002/pro.3633 (equal contribution) Raphael Carapito, Anne Molitor, Tony Prud’homme, Zhichao Miao, et al. (2019) Exome sequencing identifies a novel missense variant in CTSC causing non-syndromic aggressive periodontitis. Journal of Human Genetics 64, 689–694 Kedar Nath Natarajan^, Zhichao Miao^, Miaomiao Jiang^, et al. (2019) Comparative analysis of library and sequencing platforms for single-cell RNA-seq methods. Genome Biology 20:70, (equal contribution) https://doi.org/10.1186/s13059-019-1676-5 Maren Buttner^, Zhichao Miao^, Alexander Wolf, Sarah A Teichmann, Fabian J Theis (2019) A test metric for assessing single-cell RNA-seq batch correction. Nature Methods 16:43–49 https://doi.org/10.1038/s41592-018-0254-1 (equal contribution) Interviewed by the-scientist magazine (https://www.the-scientist.com/the-literature/computational-tools-sort-signal-from-noise-65782) Jhuma Pramanik, Xi Chen, Gozde Kar, Tomas Gomes, Johan Henriksson, Zhichao Miao, Kedar Natarajan, Andrew N. J. McKenzie, Bidesh Mahata, Sarah A. Teichmann (2018) The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation Genome Medicine. 10:76 Cao Y, Dai W and Miao Z (2018) Evaluation of protein-ligand docking by Cyscore. Computational Drug Discovery and Design, Methods Mol Biol, published by Springer. ISBN 978-1-4939-7755-0 doi: 10.1007/978-1-4939-7756-7 Carapito R, Konantz M, Paillard C, Miao Z, et. al. (2017) Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond-like features. J Clin Invenst. 1;127(11):4090-4103 •Recommended in F1000Prime Miao Z*, Westhof E* (2017) RNA structure: Advances and assessment of 3D structure prediction. Annu Rev Biophys. 46:483-503. (corresponding author) •Recommended in F1000Prime Miao Z*, et. al (2017) RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA, doi:10.1261/rna.060368.116. (corresponding author) •Recommended in F1000Prime as being of special significance in its field. Miao Z*, Cao Y (2016) Quantifying side-chain conformational variations in protein structure. Scientific Reports, 6, 37024; doi: 10.1038/srep37024. (corresponding author) Liu J^, Miao Z^, Li L, Xiao Z, Cao Y (2016) DRSP: a structural database for single residue substitutions in PDB. Progress in Biochemistry and Biophysics, 43(8): 810-816. (equal contribution) Miao Z*, Westhof E (2016) RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database. Nucleic Acids Res, 44(W1): W562-7. (corresponding author) Miao Z, Westhof E (2015) A large-scale assessment of nucleic acids binding site prediction programs. Plos Comp Biol, 11(12): e1004639. doi: 10.1371/journal.pcbi.1004639. Miao Z, Westhof E (2015) Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score. Nucleic Acids Res, 43(11):5340-51. Miao Z, Adamiak RW, Blanchet MF …, Westhof E (2015) RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. RNA, 21(6):1066-84. 10:55am - 11:25am
ID: 713 / MS-1: 3 Biological and macromolecular crystallography Oral/poster MS: Structural bioinformatics Keywords: nucleic acid structure, DNA structure, RNA structure, dinucleotide conformational class, CANA A nucleic acid structural alphabet and conformational analyses at dnatco.datmos.org Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic 11:25am - 11:45am
ID: 208 / MS-1: 4 Bursary application Oral/poster MS: Structural bioinformatics Special sessions: Introduction to machine learning Posters only: Macromolecular and biological crystallography (if it does not fit to any specific topics) Keywords: Molecular replacement, X-ray crystallography, Residue contact predictions, Model validation Applications of residue contact predictions in structural biology. 1University of Liverpool, Liverpool, United Kingdom; 2Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom; 3STFC, Rutherford Appleton Laboratory, Harwell Oxford, United Kingdom Bibliography
Sánchez Rodríguez, F. et al. ConPlot: web-based application for the visualization of protein contact maps integrated with other data, Bioinformatics (2021) https://doi.org/10.1093/bioinformatics/btab049 Sánchez Rodríguez, F. et al. Helical ensembles outperform ideal helices in molecular replacement. Acta Cryst (2020). D76, 962-970 https://doi.org/10.1107/S205979832001133X Mesdaghi S. et al. In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b. F1000Research (2021). 9:1395 https://doi.org/10.12688/f1000research.27676.2 Smetana, O. et al. High levels of auxin signalling define the stem-cell organizer of the vascular cambium. Nature 565, 485–489 (2019). doi:10.1038/s41586-018-0837-0 11:45am - 12:05pm
ID: 1285 / MS-1: 5 Biological and macromolecular crystallography Oral/poster MS: Structural bioinformatics, Integrative structural biology: The next 50 years of the Protein Data Bank, Solution scattering and combined techniques for biological systems, including component dynamics system, Structural bioinformatics Keywords: bioSAXS, bioSANS, normal mode analysis, protein docking, integrative structural bioinformatics Pepsi-SAXS/SANS - small-angle scattering-guided tools for integrative structural bioinformatics 1CNRS, Grenoble, France; 2ILL, Grenoble, France 12:05pm - 12:25pm
ID: 700 / MS-1: 6 Biological and macromolecular crystallography Oral/poster MS: Validation of cryoEM structures and maps, Structural bioinformatics Keywords: Structural biolog, structural dynamics, macromolecular disorder Refactoring the B-factor: intuitively extracting structural dynamics from macromolecular disorder 1Free University of Amsterdam, Amsterdam, The Netherlands; 2Utrecht University, Utrecht, The Netherlands 12:25pm - 12:45pm
ID: 668 / MS-1: 7 Theory, computation, modelling, data, standards Oral/poster MS: Structural bioinformatics Keywords: RNA, RNA-protein, modeling, crystallography, cryo-EM Computational modeling of RNA 3D structures and RNA-protein complexes, with the use of experimental data International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland | ||
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