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: 1st Nov 2024, 12:21:21am CET

 
 
Session Overview
Session
MS-1: Structural bioinformatics
Time:
Sunday, 15/Aug/2021:
10:20am - 12:45pm

Session Chair: Janusz Marek Bujnicki
Session Chair: Jiri Cerny
Location: Club B

50 1st floor

Invited:  Zhichao Miao (UK)


Session Abstract

For all abstracts of the session as prepared for Acta Crystallographica see PDF in Introduction, or individual abstracts below.


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Presentations
10:20am - 10:25am
ID: 1728 / MS-1: 1
Introduction
Oral/poster

Introduction to session

Janusz Bujnicki, Jiří Černý



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

Zhichao Miao1,2,3

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

Bohdan Schneider

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.

Filomeno Sanchez Rodriguez1,2, Ronan Keegan3, Melanie Vollmar2, Gwyndaf Evans2, Daniel Rigden1

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

Sergei Grudinin1, Anne Martel2, Sylvain Prevost2

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

Nicholas M Pearce1, Piet Gros2

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

Janusz Marek Bujnicki

International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland



 
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